Long non-coding RNA

7701: 31: 1490:. In general, imprinted genes are clustered together on chromosomes, suggesting the imprinting mechanism acts upon local chromosome domains rather than individual genes. These clusters are also often associated with long ncRNAs whose expression is correlated with the repression of the linked protein-coding gene on the same allele. Indeed, detailed analysis has revealed a crucial role for the ncRNAs 1860:, and our evolving understanding of its structure may inform a reinterpretation of the functional basis for many natural polymorphisms associated with disease states. Many SNPs associated with certain disease conditions are found within non-coding regions and the complex networks of non-coding transcription within these regions make it particularly difficult to elucidate the functional effects of 81:(snoRNAs), and other short RNAs. Given that some lncRNAs have been reported to have the potential to encode small proteins or micro-peptides, the latest definition of lncRNA is a class of RNA molecules of over 200 nucleotides that have no or limited coding capacity. Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences of lncRNA which do not overlap protein-coding genes. 1598:. These ncRNAs are heterogeneous in length, transcribed from several sub-telomeric loci and physically localise to telomeres. Their association with chromatin, which suggests an involvement in regulating telomere specific heterochromatin modifications, is repressed by SMG proteins that protect chromosome ends from telomere loss. In addition, TelRNAs block 1526:. A differentially methylated imprinting centre also overlaps the promoter of a long antisense ncRNA Air that is responsible for the silencing of neighbouring genes at the Igf2r locus on the paternal chromosome. The presence of allele-specific histone methylation at the Igf2r locus suggests Air also mediates silencing via chromatin modification. 887:. The recruitment of TLS to the promoter of cyclin D1 is directed by long ncRNAs expressed at low levels and tethered to 5' regulatory regions in response to DNA damage signals. Moreover, these local ncRNAs act cooperatively as ligands to modulate the activities of TLS. In the broad sense, this mechanism allows the cell to harness 160:-specific, as opposed to only ~19% of mRNAs. Only 3.6% of human lncRNA genes are expressed in various biological contexts and 34% of lncRNA genes are expressed at high level (top 25% of both lncRNAs and mRNAs) in at least one biological context. In addition to higher tissue specificity, lncRNAs are characterized by higher 845:

fulfill enhancer functions suggest Evf-2 may be illustrative of a generalised mechanism that regulates developmental genes with complex expression patterns during vertebrate growth. Indeed, the transcription and expression of similar non-coding ultraconserved elements was shown to be abnormal in human

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is relatively unknown. For example, the ncRNAs HIS-1 and BIC have been implicated in cancer development and growth control, but their function in normal cells is unknown. In addition to cancer, ncRNAs also exhibit aberrant expression in other disease states. Overexpression of PRINS is associated with

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in protein transcription factors. The Alu RNA contains two 'arms', each of which may bind one RNAP II molecule, as well as two regulatory domains that are responsible for RNAP II transcriptional repression in vitro. These two loosely structured domains may even be concatenated to other ncRNAs such as

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genes during forebrain development. Evf-2 then recruits the Dlx2 transcription factor to the same ultra-conserved element whereby Dlx2 subsequently induces expression of Dlx5. The existence of other similar ultra- or highly conserved elements within the mammalian genome that are both transcribed and

5271:

Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik SE, Shimizu M, Tili E, Rossi S, Taccioli C, Pichiorri F, Liu X, Zupo S, Herlea V, Gramantieri L, Lanza G, Alder H, Rassenti L, Volinia S, Schmittgen TD, Kipps TJ, Negrini M, Croce CM (September 2007).

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Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R

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by mitigating apoptosis and subsequently expanding the number of malignant cells in colorectal cancers. Many of these transcribed ultraconserved sites that exhibit distinct signatures in cancer are found at fragile sites and genomic regions associated with cancer. It seems likely that the aberrant

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loci are maternally inherited, except the paternally expressed antisense ncRNA Kcnqot1. Transgenic mice with truncated Kcnq1ot fail to silence the adjacent genes, suggesting that Kcnqot1 is crucial to the imprinting of genes on the paternal chromosome. It appears that Kcnqot1 is able to direct the

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transcripts that often include protein-coding genes, giving rise to a complex hierarchy of overlapping isoforms. Genomic sequences within these transcriptional foci are often shared within a number of coding and non-coding transcripts in the sense and antisense directions For example, 3012 out of

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Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T,

9193:

Reis EM, Nakaya HI, Louro R, Canavez FC, Flatschart AV, Almeida GT, Egidio CM, Paquola AC, Machado AA, Festa F, Yamamoto D, Alvarenga R, da Silva CC, Brito GC, Simon SD, Moreira-Filho CA, Leite KR, Camara-Lopes LH, Campos FS, Gimba E, Vignal GM, El-Dorry H, Sogayar MC, Barcinski MA, da Silva AM,

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and its overexpression is an early prognostic marker for poor patient survival rates. LncRNAs such as HEAT2 or KCNQ1OT1 have been shown to be regulated in the blood of patients with cardiovascular diseases such as heart failure or coronary artery disease and, moreover, to predict cardiovascular

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where they may similarly regulate global changes to gene expression. The ability of Alu and B2 RNA to bind directly to RNAP II provides a broad mechanism to repress transcription. Nevertheless, there are specific exceptions to this global response where Alu or B2 RNAs are not found at activated

9704:

Shirasawa S, Harada H, Furugaki K, Akamizu T, Ishikawa N, Ito K, Ito K, Tamai H, Kuma K, Kubota S, Hiratani H, Tsuchiya T, Baba I, Ishikawa M, Tanaka M, Sakai K, Aoki M, Yamamoto K, Sasazuki T (October 2004). "SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT, determine

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etiology, exhibits elevated expression in several regions of the brain in individuals with Alzheimer's disease Alteration of the expression of ncRNAs may also mediate changes at an epigenetic level to affect gene expression and contribute to disease aetiology. For example, the induction of an

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Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engström PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM,

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Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR (May 2005). "Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution".

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and exist in asynchronous DNA replication domains. Although the mechanism of ASAR function is still under investigation, it is hypothesized that they work via similar mechanisms as the Xist lncRNA, but on smaller autosomal domains resulting in allele specific changes in gene expression.

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have antisense partners, including many tumour suppressor genes that are frequently silenced by epigenetic mechanisms in cancer. A recent study observed an inverse expression profile of the p15 gene and an antisense ncRNA in leukaemia. A detailed analysis showed the p15 antisense ncRNA

1457:, underscoring the complexity of recently published genomic maps. Indeed, the prevalence of long ncRNAs associated with protein coding genes may contribute to localised patterns of chromatin modifications that regulate gene expression during development. For example, the majority of 1875:

The ability of long ncRNAs to regulate associated protein-coding genes may contribute to disease if misexpression of a long ncRNA deregulates a protein coding gene with clinical significance. In similar manner, an antisense long ncRNA that regulates the expression of the sense

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data shows more than 40% of transcripts are non-polyadenylated). Identifying ncRNAs within these cDNA libraries is challenging since it can be difficult to distinguish protein-coding transcripts from non-coding transcripts. It has been suggested through multiple studies that

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Mitsuya K, Meguro M, Lee MP, Katoh M, Schulz TC, Kugoh H, Yoshida MA, Niikawa N, Feinberg AP, Oshimura M (July 1999). "LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids".

1466:) was able to induce changes to heterochromatin and DNA methylation status of p15 by an unknown mechanism, thereby regulating p15 expression. Therefore, misexpression of the associated antisense ncRNAs may subsequently silence the tumour suppressor gene contributing towards 7010:

Lewejohann L, Skryabin BV, Sachser N, Prehn C, Heiduschka P, Thanos S, Jordan U, Dell'Omo G, Vyssotski AL, Pleskacheva MG, Lipp HP, Tiedge H, Brosius J, Prior H (September 2004). "Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice".

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into endo-siRNAs. Also, long ncRNAs that form extended intramolecular hairpins may be processed into siRNAs, compellingly illustrated by the esi-1 and esi-2 transcripts. Endo-siRNAs generated from these transcripts seem particularly useful in suppressing the spread of

895:, and integrate their function in transcriptional programs. Nascent long ncRNAs have been shown to increase the activity of CREB binding protein, which in turn increases the transcription of that ncRNA. A study found that a lncRNA in the antisense direction of the 1045:

throughout the mammalian genome may be partly due to these functional domains being co-opted into other long ncRNAs during evolution, with the presence of functional repeat sequence domains being a common characteristic of several known long ncRNAs including

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Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (June 2007).

1769:. Intronic antisense ncRNAs with expression correlated to the degree of tumor differentiation in prostate cancer samples have also been reported. Despite a number of long ncRNAs having aberrant expression in cancer, their function and potential role in 1452:

and EED, contain RNA binding domains that may potentially bind HOTAIR and probably other similar ncRNAs. This example nicely illustrates a broader theme whereby ncRNAs recruit the function of a generic suite of chromatin modifying proteins to specific

7276:

Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE (August 2007).

1650:). Gene mutations or variation in expression levels of such RNAs can lead to local DNA repair defects, increasing the chromosome aberration frequency. Moreover, it was demonstrated that some RNAs could stimulate long-range chromosomal rearrangements. 744:

Despite claims that the majority of long noncoding RNAs in mammals are likely to be functional, it seems likely that most of them are transcriptional noise and only a relatively small proportion has been demonstrated to be biologically relevant.

2055:"We're calling long noncoding RNAs a class, when actually the only definition is that they are longer than 200 bp," says Ana Marques, a Research Fellow at the University of Oxford who uses evolutionary approaches to understand lncRNA function. 1389:

domains. While it has been known for some time that RNA is an integral component of chromatin, it is only recently that we are beginning to appreciate the means by which RNA is involved in pathways of chromatin modification. For example,

2715:

Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Li R, Qiao J, Tang F (September 2013). "Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells".

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Liu Y, Sanoff HK, Cho H, Burd CE, Torrice C, Mohlke KL, Ibrahim JG, Thomas NE, Sharpless NE (April 2024). "Distinct Plasma Extracellular Vesicle Transcriptomes in Acute Decompensated Heart Failure Subtypes: A Liquid Biopsy Approach".

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and other parts of the brain, regulating correct brain development and function. In 2022, a comprehensive integration of lncRNAs from existing databases, revealed that there are 95,243 lncRNA genes and 323,950 transcripts in humans.

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Matsumoto A, Pasut A, Matsumoto M, Yamashita R, Fung J, Monteleone E, Saghatelian A, Nakayama KI, Clohessy JG, Pandolfi PP (January 2017). "mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide".

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were later designated as genuine ncRNA variants of protein-coding cDNAs. While the abundance and conservation of these arrangements suggest they have biological relevance, the complexity of these foci frustrates easy evaluation.

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Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM (November 2006).

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the C-terminal domain of RNAP II, repressing global elongation under stressful conditions. These examples, which bypass specific modes of regulation at individual promoters provide a means of quickly affecting global changes in

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Umlauf D, Goto Y, Cao R, Cerqueira F, Wagschal A, Zhang Y, Feil R (December 2004). "Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes".

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at the sequence level. There have been several attempts to delineate the different categories of selection signatures seen amongst lncRNAs including: lncRNAs with strong sequence conservation across the entire length of the

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differentiation. Xist expression is followed by irreversible layers of chromatin modifications that include the loss of the histone (H3K9) acetylation and H3K4 methylation that are associated with active chromatin, and the

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with the target mRNA. The formation of RNA duplexes between complementary ncRNA and mRNA may mask key elements within the mRNA required to bind trans-acting factors, potentially affecting any step in post-transcriptional

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Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (March 2009).

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Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH (June 2008).

1423:. Similar models have been proposed in mammals, where strong epigenetic mechanisms are thought to underlie the embryonic expression profiles of the Hox genes that persist throughout human development. Indeed, the human 156:, which is explained by higher cell-to-cell variation of expression levels of lncRNA genes in the individual cells, when compared to protein-coding genes. In general, the majority (~78%) of lncRNAs are characterized as 5230:

Pibouin L, Villaudy J, Ferbus D, Muleris M, Prospéri MT, Remvikos Y, Goubin G (February 2002). "Cloning of the mRNA of overexpression in colon carcinoma-1: a sequence overexpressed in a subset of colon carcinomas".

9481:"Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF" 676:, although there is disagreement about the correct method for analyzing ribosome profiling data. Additionally, it is thought that many of the peptides produced by lncRNAs may be highly unstable and without 9789:

Tufarelli C, Stanley JA, Garrick D, Sharpe JA, Ayyub H, Wood WG, Higgs DR (June 2003). "Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease".

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elements, depleted in substitution and insertion/deletion rates and depleted in rare frequency variants, indicative of purifying selection maintaining lncRNA function. However, further investigations into

1029:, where they then bind to RNAP II with high affinity and prevent the formation of active pre-initiation complexes. This allows for the broad and rapid repression of gene expression in response to stress. 1427:

are associated with hundreds of ncRNAs that are sequentially expressed along both the spatial and temporal axes of human development and define chromatin domains of differential histone methylation and

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to protein-coding genes. This prompted the authors to posit a 'cogene/gene' functional regulatory network, showing that one of these ncRNAs, 21A, regulates the expression of its antisense partner gene,

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condensation (DRT/DMC) of the entire chromosome. DRT/DMC results in chromosomal segregation errors that lead to increased frequency of secondary rearrangements and an unstable chromosome. Similar to

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also suggest a role for BC1 in targeted translational repression. Indeed, it was recently shown that BC1 is associated with translational repression in dendrites to control the efficiency of dopamine

1575:, which is expressed from the future active chromosome and able to repress Xist expression by the generation of endogenous siRNA. Together these ncRNAs ensure that only one X-chromosome is active in 1436:, that originates from the HOXC locus represses transcription across 40 kb of the HOXD locus by altering chromatin trimethylation state. HOTAIR is thought to achieve this by directing the action of 1708:

While many association studies have identified unusual expression of long ncRNAs in disease states, there is little understanding of their role in causing disease. Expression analyses that compare

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as well as H2AK119 monoubiquitylation. These modifications coincide with the transcriptional silencing of the X-linked genes. Xist RNA also localises the histone variant macroH2A to the inactive

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Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H (January 2014). "The evolution of lncRNA repertoires and expression patterns in tetrapods".

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found that all three cancers exhibited aberrant expression profiles for ultraconserved ncRNAs relative to normal cells. Further analysis of one ultraconserved ncRNA suggested it behaved like an

1594:. Telomeres have been long considered transcriptionally inert DNA-protein complexes until it was shown in the late 2000s that telomeric repeats may be transcribed as telomeric RNAs (TelRNAs) or 6381:

Singh K, Carey M, Saragosti S, Botchan M (1985). "Expression of enhanced levels of small RNA polymerase III transcripts encoded by the B2 repeats in simian virus 40-transformed mouse cells".

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Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC (December 2004). "Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana".

1150:. The existence of an RNAP III-dependent ncRNA transcriptome that regulates its RNAP II-dependent counterpart is supported by the finding of a set of ncRNAs transcribed by RNAP III with 9520:

Broadbent HM, Peden JF, Lorkowski S, Goel A, Ongen H, Green F, Clarke R, Collins R, Franzosi MG, Tognoni G, Seedorf U, Rust S, Eriksson P, Hamsten A, Farrall M, Watkins H (March 2008).

1638:(DSB) leading to chromosomal rearrangements is one of the oncogenesis's primary causes. A number of lncRNAs are crucial at the different stages of the main pathways of DSB repair in 5671:

Kwek KY, Murphy S, Furger A, Thomas B, O'Gorman W, Kimura H, Proudfoot NJ, Akoulitchev A (November 2002). "U1 snRNA associates with TFIIH and regulates transcriptional initiation".

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Lukiw WJ, Handley P, Wong L, Crapper McLachlan DR (June 1992). "BC200 RNA in normal human neocortex, non-Alzheimer dementia (NAD), and senile dementia of the Alzheimer type (AD)".

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activity in vitro and may therefore regulate telomerase activity. Although early, these studies suggest an involvement for telomeric ncRNAs in various aspects of telomere biology.

1724:(one of two overexpressed ncRNAs) is correlated with increased proliferation and colony formation suggesting an involvement in regulating cell growth. PRNCR1 was found to promote 9107:

Boeckel JN, Perret MF, Glaser SF, Seeger T, Heumüller AW, Chen W, et al. (January 2019). "Identification and regulation of the long non-coding RNA Heat2 in heart failure".

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Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (February 2007). "Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript".

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Fu X, Ravindranath L, Tran N, Petrovics G, Srivastava S (March 2006). "Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1".

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Centonze D, Rossi S, Napoli I, Mercaldo V, Lacoux C, Ferrari F, Ciotti MT, De Chiara V, Prosperetti C, Maccarrone M, Fezza F, Calabresi P, Bernardi G, Bagni C (August 2007).

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McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, Hinds DA, Pennacchio LA, Tybjaerg-Hansen A, Folsom AR, Boerwinkle E, Hobbs HH, Cohen JC (June 2007).

950:. This novel mechanism of regulating gene expression may represent a widespread method of controlling promoter usage, as thousands of RNA-DNA triplexes exist in eukaryotic 9150:

Lin R, Maeda S, Liu C, Karin M, Edgington TS (February 2007). "A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas".

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Tang RB, Wang HY, Lu HY, Xiong J, Li HH, Qiu XH, Liu HQ (February 2005). "Increased level of polymerase III transcribed Alu RNA in hepatocellular carcinoma tissue".

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Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, Okunishi R, Fukuda S, Ru K, Frith MC, Gongora MM, Grimmond SM, Hume DA, Hayashizaki Y, Mattick JS (January 2006).

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for coronary artery disease. Lately there has been increasing evidence on the role of non-coding RNAs in the development and in the categorization of heart failure.

772:, and epigenetic regulation. A further large-scale sequencing study provides evidence that many transcripts thought to be lncRNAs may, in fact, be translated into 9337:

Sonkoly E, Bata-Csorgo Z, Pivarcsi A, Polyanka H, Kenderessy-Szabo A, Molnar G, Szentpali K, Bari L, Megyeri K, Mandi Y, Dobozy A, Kemeny L, Szell M (June 2005).

3765:

Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF (February 2014).

7660:"Oplr16 serves as a novel chromatin factor to control stem cell fate by modulating pluripotency-specific chromosomal looping and TET2-mediated DNA demethylation" 704:

genomic region. Some argue that these observations suggest non-functionality of the majority of lncRNAs, while others argue that they may be indicative of rapid

84:

Long non-coding RNAs include intergenic lincRNAs, intronic ncRNAs, and sense and antisense lncRNAs, each type showing different genomic positions in relation to

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Asynchronously replicating autosomal RNAs (ASARs) are very long (~200kb) non-coding RNAs that are non-spliced, non-polyadenylated, and are required for normal

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of human lncRNAs). According to the curation of functional mechanisms of lncRNAs based on the literatures, lncRNAs are extensively reported to be involved in

700:. In other words, even when the sequence of a human lncRNA is conserved in another vertebrate species, there is often no transcription of a lncRNA in the 7113:

Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ, Brennecke J (June 2008).

7563:

Sanchez-Elsner T, Gou D, Kremmer E, Sauer F (February 2006). "Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax".

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Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. (September 2005). "The transcriptional landscape of the mammalian genome".

1079: 7719:

Mazo A, Hodgson JW, Petruk S, Sedkov Y, Brock HW (August 2007). "Transcriptional interference: an unexpected layer of complexity in gene regulation".

6010:

Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA (September 2004). "B2 RNA binds directly to RNA polymerase II to repress transcript synthesis".

3664:

Anderson DM, Anderson KM, Chang CL, Makarewich CA, Nelson BR, McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R, Olson EN (February 2015).

1552: 9194:

Verjovski-Almeida S (August 2004). "Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer".

2443:

Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR (March 2017).

108:

reveal the complexity of these transcripts in humans. The FANTOM3 project identified ~35,000 non-coding transcripts that bear many signatures of

711:

While the turnover of lncRNA transcription is much higher than initially expected, it is important to note that still, hundreds of lncRNAs are

227:

organisation, modifications, cellular locations and tissue expression profiles. Their analysis indicates human lncRNAs show a bias toward two-

8529:

Schoeftner S, Blasco MA (February 2008). "Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II".

1546:. The expression of Xist from the future inactive X-chromosome, and its subsequent coating of the inactive X-chromosome, occurs during early 9381:

Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y, Ikegawa S, Kamatani N, Hori M, Saito S, Nakamura Y, Tanaka T (2006).

6289:

Wutz A, Rasmussen TP, Jaenisch R (February 2002). "Chromosomal silencing and localization are mediated by different domains of Xist RNA".

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Li, Zhao; Liu, Lin; Jiang, Shuai; Li, Qianpeng; Feng, Changrui; Du, Qiang; Zou, Dong; Xiao, Jingfa; Zhang, Zhang; Ma, Lina (2021-01-08).

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evidence. A handful of studies have implicated long ncRNAs in a variety of disease states and support an involvement and co-operation in

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genes. This additional hierarchy of regulation that exempts individual genes from the generalised repression also involves a long ncRNA,

9522:"Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p" 1090:. This activation involves a conformational alteration of HSR-1 in response to rising temperatures, permitting its interaction with the 202:

In 2005 the landscape of the mammalian genome was described as numerous 'foci' of transcription that are separated by long stretches of

4882:

Liu, Lin; Li, Zhao; Liu, Chang; Zou, Dong; Li, Qianpeng; Feng, Changrui; Jing, Wei; Luo, Sicheng; Zhang, Zhang; Ma, Lina (2022-01-07).

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form the terminal region of mammalian chromosomes and are essential for stability and aging and play central roles in diseases such as

2759:

Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA (April 2016).

946:(DHFR) gene forms a stable RNA-DNA triplex within the major promoter of DHFR to prevent the binding of the transcriptional co-factor 5765:"Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA" 5039:"The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator" 1821:(SNPs) associated with disease states have been mapped to long ncRNAs. For example, SNPs that identified a susceptibility locus for 1522:

are recruited to the Kcnq1 loci paternal chromosome, possibly by Kcnqot1, where they may mediate gene silencing through repressive

1391: 5181:

Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA (February 2008).

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and is specifically targeted to dendrites in neurons. Sequence complementarity between BC1 and regions of various neuron-specific

9564:

Jarinova O, Stewart AF, Roberts R, Wells G, Lau P, Naing T, Buerki C, McLean BW, Cook RC, Parker JS, McPherson R (October 2009).

5476:

Halley P, Kadakkuzha BM, Faghihi MA, Magistri M, Zeier Z, Khorkova O, Coito C, Hsiao J, Lawrence M, Wahlestedt C (January 2014).

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development. Likewise, the expression of an overlapping antisense Rev-ErbAa2 transcript controls the alternative splicing of the

797:

is a tightly regulated process. Noncoding RNAs act upon different aspects of this process, targeting transcriptional modulators,

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regions of the genome but have no recognizable sequence similarity. Additionally, there have been attempts to identify conserved

9740:

Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G, Kenny PJ, Wahlestedt C (July 2008).

7861:

Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C (September 2005). "Antisense transcription in the mammalian transcriptome".

3023:

Kapranov P, Willingham AT, Gingeras TR (June 2007). "Genome-wide transcription and the implications for genomic organization".

8204:

Sleutels F, Zwart R, Barlow DP (February 2002). "The non-coding Air RNA is required for silencing autosomal imprinted genes".

9742:"Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase" 6055:"Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription" 2603:"HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell lines" 1925: 1829:(myocardial infarction associated transcript). Likewise, genome-wide association studies identified a region associated with 7623: 6664:"A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition" 6524:

Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A (December 2007). "The expanding RNA polymerase III transcriptome".

3368:"COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features" 1385:, affect many aspects of chromosomal biology, primarily including regulation of large numbers of genes by remodeling broad 5525:

Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander K, Williams RW, Jazin E (November 2010).

1094:

HSF-1, which trimerizes and induces the expression of heat shock genes. In the broad sense, these examples illustrate a

8440:

Costanzi C, Pehrson JR (June 1998). "Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals".

5315:"Mutation density analyses on long noncoding RNA reveal comparable patterns to protein-coding RNA and prognostic value" 995: 721: 17: 6195:

Mattick JS (October 2003). "Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms".

1272:

and the remodelling of neuronal networks. The RNAP III transcribed BC1 and BC200 ncRNAs, that previously derived from

1130:, uncoupling their expression from RNAP II, which they regulate. RNAP III also transcribes other ncRNAs, such as BC2, 9064:

Vausort M, Wagner DR, Devaux Y (September 2014). "Long noncoding RNAs in patients with acute myocardial infarction".

4456:

Ulitsky I (October 2016). "Evolution to the rescue: using comparative genomics to understand long non-coding RNAs".

1353:, acting as an important node that integrates various modes of long and short RNA regulation, as exemplified by the 2505:"Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses" 1595: 1403: 804:

NcRNAs modulate transcription by several mechanisms, including functioning themselves as co-regulators, modifying

8685:"ASAR15, A cis-acting locus that controls chromosome-wide replication timing and stability of human chromosome 15" 3266:

Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA, Bajic VB, Ma L, Zhang Z (January 2019).

2395:"The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression" 1765:

disease events. More recently, the highly conserved mouse homologue of MALAT1 was found to be highly expressed in

2918:

Paytuví Gallart A, Hermoso Pulido A, Anzar Martínez de Lagrán I, Sanseverino W, Aiese Cigliano R (January 2016).

128:(ORF). This number represents a conservative lower estimate, since it omitted many singleton transcripts and non- 4884:"LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system" 1658:

The discovery that long ncRNAs function in various aspects of cell biology has led to research on their role in

5370:

Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R (July 2008).

2554:"Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome" 1818: 1618:

containing ASAR6, ASAR15, or ASAR6-141 results in the same phenotype of delayed replication timing and delayed

4758: 3816:"Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes" 1761: 1741: 1350: 9339:"Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS" 1756:(also known as NEAT2) was originally identified as an abundantly expressed ncRNA that is upregulated during 5914:"Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts" 4501:"Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species" 1790: 1745: 1217: 9605:

Liu Y, Sanoff HK, Cho H, Burd CE, Torrice C, Mohlke KL, Ibrahim JG, Thomas NE, Sharpless NE (April 2009).

8736:"Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6" 7455:"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells" 3068:"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project" 2601:

Yunusov D, Anderson L, DaSilva LF, Wysocka J, Ezashi T, Roberts RM, Verjovski-Almeida S (September 2016).

7507:

Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E,

6242:"Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region" 4941:"Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae" 3868:"Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins" 1627: 931: 9833:

de Lima DS, Cardozo LE, Maracaja-Coutinho V, Suhrbier A, Mane K, Jeffries D, et al. (August 2019).

8785:

Murashko MM, Stasevich EM, Schwartz AM, Kuprash DV, Uvarova AN, Demin DE (April 2021). Blanco FJ (ed.).

1868:

and the promoter of an antisense transcript increases the expression of ZFAT not through increasing the

1345:

within the genome in the germline. However, the generation of endo-siRNAs from antisense transcripts or

1041:

B1 elements to impart their repressive role. The abundance and distribution of Alu elements and similar

1010:

have succeeded in becoming the most abundant mobile elements within the genomes, comprising ~10% of the

206:

space. While some long ncRNAs are located within the intergenic stretches, the majority are overlapping

5087: 4259:

Struhl K (February 2007). "Transcriptional noise and the fidelity of initiation by RNA polymerase II".

3466:"PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme" 3066:

Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al. (June 2007).

1399: 1062: 999: 769: 9607:"INK4/ARF transcript expression is associated with chromosome 9p21 variants linked to atherosclerosis" 8393:"The region 3′ to Xist mediates X chromosome counting and H3 Lys-4 dimethylation within the Xist gene" 8257:"Bidirectional action of the Igf2r imprint control element on upstream and downstream imprinted genes" 6113:

Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA (February 2008).

1571:

There are additional ncRNAs that are also present at the Xist loci, including an antisense transcript

808:

activity, or regulating the association and activity of co-regulators. For example, the noncoding RNA

660:

There has been considerable debate about whether lncRNAs have been misannotated and do in fact encode

4991:

Goodrich JA, Kugel JF (August 2006). "Non-coding-RNA regulators of RNA polymerase II transcription".

4405:

Chen J, Shishkin AA, Zhu X, Kadri S, Maza I, Guttman M, Hanna JH, Regev A, Garber M (February 2016).

3417:"Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts" 1886: 1689:

and non-Alzheimer's dementia (NAD) ; this early work was based on the prior identification of a

1221: 1167:

In addition to regulating transcription, ncRNAs also control various aspects of post-transcriptional

994:

The ability to quickly mediate global changes is also apparent in the rapid expression of non-coding

959: 947: 639: 207: 7025: 6963:"The brain cytoplasmic RNA BC1 regulates dopamine D2 receptor-mediated transmission in the striatum" 6209: 5863:

Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, et al. (December 2002).

4939:

Smith JE, Alvarez-Dominguez JR, Kline N, Huynh NJ, Geisler S, Hu W, Coller J, Baker KE (June 2014).

4830:

Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME (January 2015).

3125:"PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model" 7513:"Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs" 3123:

Li A, Zhou H, Xiong S, Li J, Mallik S, Fei R, Liu Y, Zhou H, Wang X, Hei X, Wang L (October 2024).

2861:

Li, Zhao; Liu, Lin; Feng, Changrui; Qin, Yuxin; Xiao, Jingfa; Zhang, Zhang; Ma, Lina (2023-01-06).

1798: 1766: 1647: 1237: 765: 756:. Over 2600 human lncRNAs with experimental evidences have been community-curated in LncRNAWiki (a 54: 6662:

Beltran M, Puig I, Peña C, García JM, Alvarez AB, Peña R, Bonilla F, de Herreros AG (March 2008).

4691:"Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications" 2167: 9907: 5527:"Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse" 2812:"Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders" 1900:

Alongside their role in mediating pathological processes, long noncoding RNAs play a role in the

1830: 1519: 1437: 1419:, by recruiting and directing the chromatin modifying functions of the trithorax protein Ash1 to 1333: 943: 872: 833: 697: 61:

that are not translated into protein. This arbitrary limit distinguishes long ncRNAs from small

9835:"Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination" 4646:

Mercer TR, Dinger ME, Mattick JS (March 2009). "Long non-coding RNAs: insights into functions".

4599:"A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs" 3613:

Chen J, Shishkin AA, Zhu X, Kadri S, Maza I, Guttman M, Hanna JH, Regev A, Garber M (Feb 2016).

3517:"FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome" 2917: 9912: 9338: 8110:"Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes" 7020: 6712: 6204: 4173:

Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT, Marques AC (2012).

3969:"Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals" 1881: 1861: 1786: 1686: 1277: 1232:

of the antisense transcript represses splicing and induces translation of the Zeb2 mRNA during

733: 278: 223:

consortium has collated and analysed a comprehensive set of human lncRNA annotations and their

8306:"Allele-specific histone lysine methylation marks regulatory regions at imprinted mouse genes" 5183:"Ultraconservation identifies a small subset of extremely constrained developmental enhancers" 4358:"Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications" 3566:"PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions" 1822: 1811: 1678: 1440:

chromatin remodeling complexes in trans to govern the cells' epigenetic state and subsequent

1317: 1249: 864:

Local ncRNAs can also recruit transcriptional programmes to regulate adjacent protein-coding

673: 176:

In comparison to mammals relatively few studies have focused on the prevalence of lncRNAs in

161: 70: 9383:"Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction" 8023:

Braidotti G, Baubec T, Pauler F, Seidl C, Smrzka O, Stricker S, Yotova I, Barlow DP (2004).

5804:

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. (February 2001).

3217:"RNAsamba: neural network-based assessment of the protein-coding potential of RNA sequences" 1296:

and BC1 RNA-deleted mice exhibit behavioural changes with reduced exploration and increased

752:(a database of literature described lncRNAs), with the majority of these being described in 9846: 9618: 9435: 9250: 8632:

Donley N, Stoffregen EP, Smith L, Montagna C, Thayer MJ (April 2013). Bartolomei MS (ed.).

8588: 8577:"Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends" 8449: 8213: 7930: 7870: 7572: 7406: 7395:"RNA is an integral component of chromatin that contributes to its structural organization" 7347: 7290: 7186: 7126: 6817: 6390: 5876: 5817: 5440: 5383: 5372:"Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription" 5139: 5127: 4224:

Brosius J (May 2005). "Waste not, want not—transcript excess in multicellular eukaryotes".

4026:"Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs" 3980: 3723: 3268:"Characterization and identification of long non-coding RNAs based on feature relationship" 3079: 2981: 2614: 2456: 2345: 2291: 2239: 1913: 1794: 1682: 1667: 1458: 1342: 1289: 1115: 1091: 923: 876: 805: 74: 8304:

Fournier C, Goto Y, Ballestar E, Delaval K, Hever AM, Esteller M, Feil R (December 2002).

7705: 7700: 6757:"Primary structure, neural-specific expression, and dendritic location of human BC200 RNA" 6115:"Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock" 5716:"Specific double-stranded RNA interference in undifferentiated mouse embryonic stem cells" 4126:"Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals" 3319:"CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model" 2503:

Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (September 2011).

2121:"The contribution of databases towards understanding the universe of long non-coding RNAs" 1486:, whereby only one allele of a gene is expressed from either the maternal or the paternal 8: 6912:

Wang H, Iacoangeli A, Lin D, Williams K, Denman RB, Hellen CU, Tiedge H (December 2005).

6240:

Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, Kanduri C (June 2008).

1635: 1547: 1523: 1515: 1378: 1370: 1329: 1313: 1269: 1075: 1026: 955: 939: 935: 888: 696:

lncRNAs revealed that while lncRNAs are conserved in sequence, they are not conserved in

446: 9850: 9622: 9439: 9254: 8634:"Asynchronous replication, mono-allelic expression, and long range Cis-effects of ASAR6" 8592: 8453: 8217: 7934: 7874: 7704: This article incorporates text from this source, which is available under the 7576: 7410: 7351: 7294: 7190: 7130: 6821: 6394: 5880: 5821: 5444: 5387: 5347: 5314: 5143: 4748: 4731: 4075:"Mutations within lncRNAs are effectively selected against in fruitfly but not in human" 3984: 3727: 3151: 3124: 3083: 2985: 2618: 2460: 2349: 2295: 2243: 2173: 1518:

and actually resides within a Kcnq1 sense exon. Similar to HOTAIR (see above), Eed-Ezh2

906:

Recent evidence has raised the possibility that transcription of genes that escape from

9869: 9834: 9815: 9766: 9741: 9641: 9606: 9456: 9423: 9314: 9297: 9219: 9175: 9132: 9089: 9041: 9016: 8910: 8862: 8837: 8813: 8786: 8762: 8735: 8711: 8684: 8660: 8633: 8614: 8554: 8473: 8417: 8392: 8237: 8186: 8134: 8109: 8049: 8024: 8000: 7975: 7951: 7918: 7894: 7788: 7763: 7744: 7684: 7659: 7640: 7632: 7596: 7537: 7512: 7484: 7429: 7394: 7311: 7278: 7255: 7207: 7174: 7147: 7114: 7090: 7065: 7046: 6987: 6962: 6938: 6913: 6889: 6864: 6781: 6772: 6756: 6688: 6663: 6636: 6611: 6503: 6457: 6414: 6363: 6314: 6266: 6241: 6079: 6054: 6035: 5989: 5696: 5601: 5553: 5526: 5502: 5477: 5404: 5371: 5207: 5182: 5163: 5063: 5038: 5016: 4965: 4940: 4916: 4883: 4856: 4831: 4807: 4782: 4671: 4623: 4598: 4574: 4549: 4525: 4500: 4481: 4433: 4407:"Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs" 4406: 4382: 4357: 4333: 4306: 4284: 4201: 4174: 4150: 4125: 4101: 4074: 4050: 4025: 4001: 3968: 3943: 3919:"Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins" 3918: 3894: 3867: 3840: 3815: 3791: 3766: 3747: 3690: 3665: 3641: 3615:"Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs" 3614: 3590: 3565: 3541: 3516: 3492: 3465: 3441: 3416: 3392: 3367: 3343: 3318: 3243: 3216: 3100: 3067: 3048: 3005: 2944: 2919: 2895: 2862: 2838: 2811: 2787: 2760: 2741: 2692: 2659: 2635: 2602: 2578: 2553: 2529: 2504: 2477: 2444: 2419: 2394: 2369: 2315: 2263: 2200: 2175: 2156: 2096: 2071: 2000: 1973: 1712:

and normal cells have revealed changes in the expression of ncRNAs in several forms of

1495: 1483: 1229: 1220:

for efficient translation. The retention of the intron depends on the expression of an

1127: 1095: 1087: 1042: 1022: 761: 712: 688: 687:

Initial studies into lncRNA conservation noted that as a class, they were enriched for

677: 669: 404: 149:

type. Using FANTOM5, 27,919 long ncRNAs have been identified in various human sources.

125: 9678: 9273: 9238: 8954: 8929: 8330: 8305: 8281: 8256: 7917:

Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H (January 2008).

7837: 7812: 7370: 7335: 6865:"Activity-dependent regulation of dendritic BC1 RNA in hippocampal neurons in culture" 6729: 6350: 6333: 5938: 5913: 5781: 5764: 5645: 5620: 5274:"Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas" 5244: 3666:"A micropeptide encoded by a putative long noncoding RNA regulates muscle performance" 672:

studies have suggested that anywhere from 40% to 90% of annotated lncRNAs are in fact

9874: 9807: 9771: 9722: 9686: 9646: 9587: 9543: 9502: 9461: 9404: 9363: 9319: 9278: 9223: 9211: 9167: 9124: 9081: 9046: 8997: 8959: 8902: 8867: 8818: 8767: 8716: 8665: 8606: 8546: 8508: 8477: 8465: 8422: 8373: 8335: 8286: 8229: 8178: 8139: 8090: 8054: 8005: 7956: 7886: 7842: 7793: 7736: 7689: 7615: 7588: 7542: 7476: 7434: 7375: 7316: 7247: 7212: 7152: 7095: 7038: 6992: 6943: 6894: 6845: 6840: 6805: 6786: 6734: 6693: 6641: 6592: 6551: 6495: 6449: 6406: 6355: 6306: 6271: 6222: 6177: 6136: 6084: 6027: 5981: 5943: 5894: 5845: 5786: 5745: 5740: 5731: 5715: 5688: 5650: 5593: 5558: 5507: 5458: 5409: 5352: 5334: 5295: 5248: 5212: 5155: 5107: 5068: 5008: 4970: 4921: 4903: 4861: 4812: 4763: 4712: 4663: 4628: 4579: 4530: 4473: 4438: 4387: 4338: 4276: 4241: 4206: 4155: 4106: 4055: 4006: 3948: 3899: 3845: 3796: 3751: 3739: 3695: 3646: 3595: 3546: 3497: 3446: 3397: 3348: 3299: 3248: 3197: 3156: 3105: 3040: 2997: 2970:"RNA maps reveal new RNA classes and a possible function for pervasive transcription" 2969: 2949: 2900: 2882: 2843: 2792: 2733: 2697: 2679: 2640: 2583: 2534: 2482: 2424: 2361: 2307: 2255: 2205: 2160: 2148: 2140: 2101: 2046: 2005: 1909: 1749: 1662:. Tens of thousands of lncRNAs are potentially associated with diseases based on the 1151: 1147: 1135: 1119: 927: 896: 854: 798: 794: 101: 9237:

Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E, Dahlberg JE (March 2005).

9136: 9093: 8914: 8618: 8190: 7898: 7748: 7600: 7259: 7050: 6507: 6461: 6367: 6318: 6039: 5993: 5700: 5020: 4832:"lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs" 4675: 4485: 4288: 3581: 3284: 3267: 3009: 2745: 2319: 938:

or involved in transcription elongation. A ncRNA transcribed from an upstream minor

9864: 9854: 9819: 9799: 9761: 9753: 9714: 9682: 9674: 9636: 9626: 9577: 9533: 9492: 9451: 9443: 9394: 9353: 9309: 9268: 9258: 9203: 9179: 9159: 9116: 9073: 9036: 9028: 8989: 8949: 8941: 8894: 8857: 8849: 8808: 8798: 8757: 8747: 8706: 8696: 8655: 8645: 8596: 8558: 8538: 8500: 8457: 8412: 8404: 8365: 8325: 8317: 8276: 8268: 8241: 8221: 8170: 8129: 8121: 8082: 8044: 8036: 7995: 7987: 7946: 7938: 7878: 7832: 7824: 7783: 7775: 7728: 7679: 7671: 7611: 7607: 7580: 7532: 7524: 7488: 7466: 7424: 7414: 7365: 7355: 7306: 7298: 7239: 7202: 7194: 7142: 7134: 7085: 7077: 7030: 6982: 6978: 6974: 6933: 6925: 6884: 6876: 6835: 6825: 6776: 6768: 6724: 6683: 6675: 6631: 6623: 6582: 6541: 6533: 6487: 6441: 6418: 6398: 6345: 6298: 6261: 6253: 6214: 6167: 6126: 6074: 6066: 6019: 5973: 5933: 5925: 5884: 5835: 5825: 5776: 5735: 5727: 5680: 5640: 5632: 5605: 5585: 5548: 5538: 5497: 5489: 5448: 5399: 5391: 5342: 5326: 5285: 5240: 5202: 5194: 5167: 5147: 5099: 5058: 5050: 5000: 4960: 4952: 4911: 4895: 4851: 4843: 4802: 4794: 4753: 4743: 4702: 4655: 4618: 4610: 4569: 4561: 4520: 4512: 4465: 4428: 4418: 4377: 4369: 4328: 4318: 4268: 4233: 4196: 4186: 4145: 4137: 4096: 4086: 4045: 4037: 3996: 3988: 3938: 3930: 3889: 3879: 3835: 3827: 3786: 3778: 3731: 3685: 3677: 3636: 3626: 3585: 3577: 3536: 3528: 3487: 3477: 3436: 3428: 3415:

Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y (September 2013).

3387: 3379: 3338: 3330: 3289: 3279: 3238: 3228: 3187: 3146: 3136: 3095: 3087: 3052: 3032: 2989: 2939: 2931: 2890: 2874: 2833: 2823: 2782: 2772: 2725: 2687: 2671: 2630: 2622: 2573: 2565: 2524: 2516: 2472: 2464: 2414: 2406: 2373: 2353: 2299: 2267: 2247: 2195: 2187: 2132: 2091: 2083: 2036: 1995: 1985: 1974:"Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease" 1894: 1877: 1838: 1677:

The first published report of an alteration in lncRNA abundance in aging and human

1639: 1615: 1605: 1454: 1143: 1065:

elements (including Alu, B1, and B2 RNAs) increases during cellular stress such as

157: 146: 9497: 9480: 9298:"Expression of the putative proto-oncogene His-1 in normal and neoplastic tissues" 9077: 4550:"Evolutionary conservation of long non-coding RNAs; sequence, structure, function" 2863:"LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations" 1782:

of psoriatic patients compared with both psoriatic lesions and healthy epidermis.

1032:

A dissection of the functional sequences within Alu RNA transcripts has drafted a

736:

in lncRNAs, though these studies have currently given way to conflicting results.

9897: 9631: 9566:"Functional analysis of the chromosome 9p21.3 coronary artery disease risk locus" 8701: 8650: 7508: 7419: 7081: 6172: 6155: 6131: 6114: 5493: 4956: 4565: 4516: 4499:

Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP, Ulitsky I (May 2015).

4191: 3515:

Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, et al. (May 2017).

1901: 1890: 1846: 1733: 1717: 1611: 1441: 1374: 1185: 1168: 1099: 1066: 988: 983: 963: 865: 129: 121: 9120: 7279:"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells" 6571:"Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5" 3192: 3175: 2761:"Single-cell analysis of long non-coding RNAs in the developing human neocortex" 1872:

stability, but rather by repressing the expression of the antisense transcript.

1204:

of mRNA can induce its translation and functionally diversify the repertoire of

9839:

Proceedings of the National Academy of Sciences of the United States of America

9582: 9565: 9243:

Proceedings of the National Academy of Sciences of the United States of America

9032: 8575:

Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J (November 2007).

7528: 7471: 7454: 7340:

Proceedings of the National Academy of Sciences of the United States of America

6810:

Proceedings of the National Academy of Sciences of the United States of America

5330: 3934: 3831: 3767:"Toddler: an embryonic signal that promotes cell movement via Apelin receptors" 3681: 3141: 2136: 1770: 1535: 1429: 1281: 1280:, respectively. BC1 expression is induced in response to synaptic activity and 1086:

in an inactive state, but upon stress is activated to induce the expression of

1083: 1037: 907: 829: 536: 370: 332: 142: 113: 62: 9399: 9382: 8391:

Morey C, Navarro P, Debrand E, Avner P, Rougeulle C, Clerc P (February 2004).

8369: 7991: 7034: 6627: 6537: 6478:

Shamovsky I, Nudler E (October 2006). "Gene control by large noncoding RNAs".

5290: 5273: 4423: 4373: 4237: 3631: 2777: 1972:

Fernandes JC, Acuña SM, Aoki JI, Floeter-Winter LM, Muxel SM (February 2019).

9891: 9479:

Pasmant E, Laurendeau I, Héron D, Vidaud M, Vidaud D, Bièche I (April 2007).

8504: 8408: 8108:

Mancini-Dinardo D, Steele SJ, Levorse JM, Ingram RS, Tilghman SM (May 2006).

6491: 5929: 5543: 5338: 4907: 4323: 4091: 3482: 3176:"DeepPlnc: Bi-modal deep learning for highly accurate plant lncRNA discovery" 2886: 2683: 2144: 1940: 1869: 1857: 1737: 1416: 1285: 858: 604: 484: 468: 153: 109: 9859: 9447: 9263: 8993: 8601: 8576: 7882: 7584: 7198: 5636: 5103: 4175:"Rapid turnover of long noncoding RNAs and the evolution of gene expression" 3782: 3233: 2993: 2303: 2251: 1332:

of complementary sequences, such as antisense or repetitive regions between

930:

transcription of all genes. These general factors include components of the

9902: 9878: 9811: 9775: 9726: 9690: 9650: 9591: 9547: 9506: 9465: 9408: 9367: 9358: 9282: 9215: 9207: 9171: 9163: 9128: 9085: 9050: 9001: 8871: 8822: 8771: 8752: 8720: 8669: 8610: 8550: 8512: 8426: 8377: 8339: 8321: 8290: 8233: 8182: 8143: 8094: 8086: 8058: 8040: 8009: 7960: 7890: 7828: 7813:"Point mutations in the WD40 domain of Eed block its interaction with Ezh2" 7797: 7740: 7693: 7619: 7592: 7546: 7480: 7438: 7320: 7251: 7216: 7156: 7099: 7042: 6996: 6947: 6880: 6830: 6752: 6713:"Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA" 6697: 6645: 6596: 6587: 6570: 6555: 6499: 6453: 6359: 6310: 6275: 6226: 6181: 6140: 6088: 6031: 5985: 5898: 5849: 5790: 5749: 5692: 5597: 5562: 5511: 5462: 5413: 5356: 5299: 5252: 5216: 5159: 5111: 5072: 5012: 4974: 4925: 4865: 4816: 4767: 4716: 4667: 4632: 4583: 4534: 4477: 4442: 4391: 4342: 4280: 4245: 4210: 4159: 4110: 4059: 4010: 3952: 3903: 3849: 3800: 3743: 3699: 3650: 3599: 3550: 3501: 3450: 3401: 3352: 3303: 3252: 3201: 3160: 3109: 3044: 3001: 2953: 2904: 2847: 2796: 2737: 2701: 2644: 2587: 2538: 2486: 2428: 2365: 2311: 2259: 2209: 2152: 2120: 2105: 2050: 2009: 1702: 1568: 1273: 1201: 1189: 1180: 1139: 1131: 1011: 1003: 910:

might be mediated by expression of long non-coding RNA within the escaping

825: 725: 190:

approach, which also established the associated Green Non-Coding Database (

133: 117: 9323: 8963: 8906: 8469: 7846: 7675: 7629:. If this is an intentional citation to a retracted paper, please replace 7379: 7360: 6929: 6898: 6849: 6790: 6738: 6410: 6334:"Identification of new Xlsirt family members in the Xenopus laevis oocyte" 5947: 5763:

Yik JH, Chen R, Nishimura R, Jennings JL, Link AJ, Zhou Q (October 2003).

5654: 4899: 4798: 4707: 4690: 4141: 3532: 2935: 2878: 2675: 2410: 437: 285: 30: 9718: 9538: 9521: 8945: 8853: 8836:

Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, and Zhang Z (Jan 2019).

8803: 7919:"Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA" 6546: 6257: 5840: 4847: 4781:

Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (January 2011).

4732:"Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review" 4272: 3432: 3383: 3334: 2828: 2520: 2191: 1990: 1905: 1826: 1789:

exhibit distinct profiles in various human cancer states. An analysis of

1709: 1539: 1382: 1358: 1225: 1070: 900: 701: 361: 180:. However an extensive study considering 37 higher plant species and six 9424:"A common allele on chromosome 9 associated with coronary heart disease" 8930:"Primate brain-specific cytoplasmic transcript of the Alu repeat family" 8125: 7942: 7779: 7302: 7138: 5889: 5864: 5589: 5395: 5151: 5054: 4469: 3992: 3884: 3735: 3294: 3091: 2468: 2357: 9832: 9017:"PRNCR1: a long non-coding RNA with a pivotal oncogenic role in cancer" 8898: 8272: 7732: 7243: 6804:

Tiedge H, Fremeau RT, Weinstock PH, Arancio O, Brosius J (March 1991).

6679: 6218: 6070: 5478:"Regulation of the apolipoprotein gene cluster by a long noncoding RNA" 5198: 4614: 4041: 2569: 1807: 1778:

susceptibility, with PRINS expression being elevated in the uninvolved

1757: 1729: 1698: 1663: 1599: 1542:

is directed by one of the earliest and best characterized long ncRNAs,

1487: 1411: 1346: 1321: 1316:

duplexes can also provide a substrate for the generation of endogenous

1233: 1058: 1033: 951: 911: 693: 408: 392: 354: 323: 212: 203: 58: 8787:"The Role of RNA in DNA Breaks, Repair and Chromosomal Rearrangements" 8255:

Zwart R, Sleutels F, Wutz A, Schinkel AH, Barlow DP (September 2001).

5621:"A monoclonal antibody to triplex DNA binds to eucaryotic chromosomes" 5619:

Lee JS, Burkholder GD, Latimer LJ, Haug BL, Braun RP (February 1987).

3917:

Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES (July 2013).

2729: 2626: 2087: 2041: 2024: 7976:"Silencing by imprinted noncoding RNAs: is transcription the answer?" 6445: 6402: 5830: 5805: 2176:"The functions and unique features of long intergenic non-coding RNA" 1950: 1850: 1842: 1779: 1775: 1694: 1587: 1479: 1395: 1386: 1349:

may also silence the expression of their functional counterparts via

884: 850: 821: 790: 568: 316: 211:

8961 cDNAs previously annotated as truncated coding sequences within

186: 169: 165: 9421: 8542: 8225: 6023: 5453: 5428: 5004: 4659: 3036: 970:

is able to repress transcription elongation by, in combination with

9803: 9757: 8574: 8491:

Blasco MA (October 2007). "Telomere length, stem cells and aging".

8174: 5977: 5684: 5128:"In vivo enhancer analysis of human conserved non-coding sequences" 1865: 1834: 1802: 1725: 1556: 1511: 1491: 1463: 1424: 1420: 1293: 1257: 1172: 1047: 892: 846: 813: 749: 630: 224: 138: 100:

Long non-coding transcripts are found in many species. Large-scale

66: 9336: 8683:

Donley N, Smith L, Thayer MJ (January 2015). Bartolomei MS (ed.).

8461: 7175:"Intersection of the RNA interference and X-inactivation pathways" 6302: 3065: 152:

Quantitatively, lncRNAs demonstrate ~10-fold lower abundance than

8884: 5865:"Initial sequencing and comparative analysis of the mouse genome" 5862: 3317:

Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W (April 2013).

2335: 1930: 1690: 1659: 1619: 1564: 1507: 1297: 1265: 1205: 1176: 1123: 967: 883:

histone acetyltransferase activities on a repressed gene target,

773: 729: 705: 665: 661: 430: 220: 8838:"LncBook: a curated knowledgebase of human long non-coding RNAs" 8784: 6523: 6112: 4938: 3712: 2660:"LncExpDB: an expression database of human long non-coding RNAs" 1971: 1785:

Genome-wide profiling revealed that many transcribed non-coding

1606:

In regulation of DNA replication timing and chromosome stability

891:, which make up one of the largest classes within the mammalian 475: 9239:"Accumulation of miR-155 and BIC RNA in human B cell lymphomas" 9015:

Bardhan A, Banerjee A, Basu K, Pal DK, Ghosh A (January 2022).

7810: 6332:

Zearfoss NR, Chan AP, Kloc M, Allen LH, Etkin LD (April 2003).

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Camargo AP, Sourkov V, Pereira GA, Carazzolle MF (March 2020).

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Denisenko O, Shnyreva M, Suzuki H, Bomsztyk K (October 1998).

7334:

Nickerson JA, Krochmalnic G, Wan KM, Penman S (January 1989).

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Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD (June 2006).

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Wutz A, Gribnau J (October 2007). "X inactivation Xplained".

7658:

Jia L, Wang Y, Wang C, Du Z, Zhang S, Wen X, Zhang S (2020).

7562: 7333: 6803: 6239: 4689:

Dinger ME, Amaral PP, Mercer TR, Mattick JS (November 2009).

4547: 3916: 2600: 2229: 1810:

results from important functions they fulfil in normal human

1502: 1445: 1337: 1156: 1015: 1007: 880: 809: 753: 181: 177: 9478: 8303: 5229: 5180: 2391: 1614:

timing and chromosome stability. Deletion of any one of the

1248:

NcRNA may also apply additional regulatory pressures during

1098:

nested within ncRNAs whereby Alu or B2 RNAs repress general

1021:, respectively. These elements are transcribed as ncRNAs by 9563: 9519: 8979: 7916: 7115:"An endogenous small interfering RNA pathway in Drosophila" 6960: 6862: 6612:"Posttranscriptional gene regulation by long noncoding RNA" 4548:

Johnsson P, Lipovich L, Grandér D, Morris KV (March 2014).

1945: 1935: 1643: 1623: 1572: 1560: 1543: 1449: 1354: 1308:

In addition to masking key elements within single-stranded

1261: 1209: 1103: 1051: 917: 841: 837: 817: 757: 717: 228: 145:

express the greatest amount of long non-coding RNAs of any

89: 85: 9739: 8733: 7859: 6380: 4780: 3022: 1849:

and its altered expression is associated with a high-risk

1482:

modification were first apparent within the phenomenon of

1415:, long ncRNAs induce the expression of the homeotic gene, 1082:(HSR-1). It was argued that HSR-1 is present in mammalian 779: 720:, lncRNAs in which only a portion of the transcript (e.g. 27:

Non-protein coding transcripts longer than 200 nucleotides

9106: 8734:

Heskett MB, Smith LG, Spellman P, Thayer MJ (June 2020).

8254: 6911: 5803: 4829: 4688: 4172: 1309: 1102:, while other ncRNAs activate the expression of specific 294: 50: 8390: 6863:

Muslimov IA, Banker G, Brosius J, Tiedge H (June 1998).

6569:

Pagano JM, Farley BM, McCoig LM, Ryder SP (March 2007).

5762: 5618: 5524: 4783:"lncRNAdb: a reference database for long noncoding RNAs" 2809: 2551: 2502: 2280: 966:

the C-terminal domain of RNAP II. In contrast the ncRNA

760:-based, publicly editable and open-content platform for 664:. Several lncRNAs have been found to in fact encode for 7718: 7063: 6914:"Dendritic BC1 RNA in translational control mechanisms" 6568: 5313:

Zhang, Troy; Yu, Hui; Bai, Yongsheng; Guo, Yan (2023).

3965: 1864:. For example, a SNP both within the truncated form of 958:

can induce transcription by binding to and stimulating

9192: 9014: 8159: 7506: 7392: 7230:

Kiefer JC (April 2007). "Epigenetics in development".

6609: 6009: 5670: 5270: 4554:

Biochimica et Biophysica Acta (BBA) - General Subjects

4307:"Non-coding RNA: what is functional and what is junk?" 4300: 4298: 2758: 728:) is conserved, and lncRNAs that are transcribed from 8071: 7275: 6661: 6331: 6288: 6052: 5963: 5806:"Initial sequencing and analysis of the human genome" 4023: 3813: 3514: 3173: 1529: 1162: 1074:

promoters of genes undergoing induction, such as the

899:(APOA1) regulates the transcription of APOA1 through 801:

and even the DNA duplex to regulate gene expression.

9380: 9295: 7112: 7064:

Golden DE, Gerbasi VR, Sontheimer EJ (August 2008).

5911: 5714:

Yang S, Tutton S, Pierce E, Yoon K (November 2001).

5713: 5369: 5085: 4404: 4123: 3814:

Ingolia NT, Lareau LF, Weissman JS (November 2011).

3764: 3612: 3174:

Ritu, Gupta S, Kumar N, Shankar R (September 2022).

2966: 1817:

Recently, a number of association studies examining

1681:

was provided by Lukiw et al. in a study using short

1514:) to an imprinting centre that overlaps the Kcnqot1 1303: 1109: 184:

identified ~200,000 non-coding transcripts using an

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Cold Spring Harbor Symposia on Quantitative Biology

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Components of the Polycomb complex, including 9705:susceptibility to autoimmune thyroid disease". 8927: 8570: 8568: 8519: 8439: 7761: 6477: 6431: 6153: 6005: 6003: 5036: 4986: 4984: 2225: 2223: 2221: 2219: 2072:"On the classification of long non-coding RNAs" 1553:induction of repressive chromatin modifications 1336:, forms an RNA duplex that may be processed by 1240:ErbAa2 mRNA to form two antagonistic isoforms. 1134:and some microRNAs and snoRNAs, in addition to 8155: 8153: 7974:Pauler FM, Koerner MV, Barlow DP (June 2007). 7451: 7393:Rodríguez-Campos A, Azorín F (November 2007). 6657: 6655: 5856: 2714: 2174:Ransohoff JD, Wei Y, Khavari PA (March 2018). 1398:core factors by coordinating intrachromosomal 1114:Many of the ncRNAs that interact with general 1025:in response to environmental stresses such as 1006:in humans and analogous B1 and B2 elements in 9554: 8829: 8358:Current Opinion in Genetics & Development 7755: 7657: 7168: 7166: 5312: 4990: 4729: 4597:Rivas E, Clements J, Eddy SR (January 2017). 4124:Washietl S, Kellis M, Garber M (April 2014). 4072: 4024:Ponjavic J, Ponting CP, Lunter G (May 2007). 3122: 2960: 2498: 2496: 2387: 2385: 2383: 1126:, Alu and B1 and B2 RNAs) are transcribed by 9109:Journal of Molecular and Cellular Cardiology 8565: 8351: 8349: 7502: 7500: 7498: 6519: 6517: 6046: 6000: 5959: 5957: 5429:"Non-coding RNA: More uses for genomic junk" 5266: 5264: 5262: 5086:Panganiban G, Rubenstein JL (October 2002). 4981: 4774: 4736:Annual Review of Genomics and Human Genetics 4682: 4639: 3414: 2860: 2657: 2331: 2329: 2216: 2069: 1582: 1224:transcript that complements the intronic 5' 978:, forming an inactive complex that prevents 8355: 8150: 7271: 7269: 7172: 6710: 6652: 6473: 6471: 5797: 5666: 5664: 5426: 5032: 5030: 4881: 3463: 3265: 3059: 1364: 1192:, transport, translation, and degradation. 1171:. Similar to small regulatory RNAs such as 1036:structure analogous to the organization of 8975: 8973: 8928:Watson JB, Sutcliffe JG (September 1987). 8835: 7912: 7910: 7908: 7643:|...|intentional=yes}} 7558: 7556: 7163: 4304: 3564:Lin MF, Jungreis I, Kellis M (July 2011). 3408: 2493: 2380: 234: 9868: 9858: 9765: 9640: 9630: 9581: 9537: 9496: 9455: 9398: 9357: 9313: 9272: 9262: 9040: 8953: 8861: 8812: 8802: 8761: 8751: 8710: 8700: 8659: 8649: 8600: 8416: 8346: 8329: 8280: 8133: 8048: 7999: 7950: 7836: 7787: 7762:Cerase A, Tartaglia GG (September 2020). 7683: 7536: 7495: 7470: 7428: 7418: 7369: 7359: 7310: 7206: 7146: 7089: 7024: 6986: 6937: 6888: 6839: 6829: 6780: 6728: 6687: 6635: 6586: 6545: 6514: 6349: 6265: 6208: 6171: 6130: 6108: 6106: 6104: 6102: 6100: 6098: 6078: 6012:Nature Structural & Molecular Biology 5954: 5937: 5888: 5839: 5829: 5780: 5739: 5644: 5552: 5542: 5501: 5452: 5403: 5346: 5289: 5259: 5206: 5062: 4964: 4915: 4855: 4806: 4757: 4747: 4706: 4622: 4573: 4524: 4432: 4422: 4381: 4332: 4322: 4261:Nature Structural & Molecular Biology 4200: 4190: 4149: 4100: 4090: 4049: 4000: 3942: 3893: 3883: 3839: 3790: 3689: 3640: 3630: 3589: 3540: 3491: 3481: 3440: 3391: 3342: 3293: 3283: 3242: 3232: 3191: 3150: 3140: 3099: 2943: 2894: 2837: 2827: 2786: 2776: 2718:Nature Structural & Molecular Biology 2691: 2634: 2577: 2528: 2476: 2418: 2326: 2199: 2119:Ma, Lina; Zhang, Zhang (September 2023). 2095: 2040: 1999: 1989: 1394:epigenetically induces the activation of 7336:"Chromatin architecture and nuclear RNA" 7266: 6468: 6147: 5661: 5027: 3464:Li A, Zhang J, Zhou Z (September 2014). 3366:Hu L, Xu Z, Hu B, Lu ZJ (January 2017). 3365: 1889:transcript by a genetic mutation led to 918:Regulating basal transcription machinery 668:with biologically significant function. 34:Different types of long non-coding RNAs. 29: 8970: 7905: 7553: 6194: 6154:Shamovsky I, Nudler E (February 2008). 4455: 4356:Kapusta A, Feschotte C (October 2014). 4223: 2118: 1653: 1478:Many emergent themes of ncRNA-directed 1276:, are expressed in the mouse and human 1252:, a property particularly exploited in 1212:mRNA requires the retention of a 5'UTR 861:in like fashion to protein-coding RNA. 857:cells, suggesting their involvement in 832:induces transcription of Evf-2 from an 780:In the regulation of gene transcription 197: 14: 9890: 8490: 7229: 6806:"Dendritic location of neural BC1 RNA" 6095: 4258: 2180:Nature Reviews. Molecular Cell Biology 2125:Nature Reviews. Molecular Cell Biology 2022: 1893:and silencing of sense genes, causing 1705:(brain, cytoplasmic, 200 nucleotide). 1292:receptor-mediated transmission in the 593:Vertebrate, fly, mosquito, yeast, worm 7173:Ogawa Y, Sun BK, Lee JT (June 2008). 6711:Munroe SH, Lazar MA (November 1991). 4993:Nature Reviews Molecular Cell Biology 4877: 4875: 3861: 3859: 2070:Ma L, Bajic VB, Zhang Z (June 2013). 1926:List of long non-coding RNA databases 168:specificity in tissues such as human 2065: 2063: 1967: 1965: 1369:Epigenetic modifications, including 812:functions as a co-activator for the 9346:The Journal of Biological Chemistry 6717:The Journal of Biological Chemistry 6575:The Journal of Biological Chemistry 4749:10.1146/annurev-genom-112921-123710 1268:activity contributes to changes in 1264:translation of mRNA in response to 104:(cDNA) sequencing projects such as 24: 6773:10.1523/JNEUROSCI.13-06-02382.1993 4872: 3856: 1530:Xist and X-chromosome inactivation 1188:including pre-mRNA processing and 1163:In post-transcriptional regulation 998:. The short interspersed nuclear ( 194:), a repository of plant lncRNAs. 25: 9924: 9679:10.1161/CIRCULATIONAHA.123.065513 9302:The American Journal of Pathology 6755:, Chen W, Brosius J (June 1993). 4305:Palazzo AF, Lee ES (2015-01-26). 4073:Haerty W, Ponting CP (May 2013). 2060: 1962: 1432:accessibility. One ncRNA, termed 1304:In siRNA-directed gene regulation 1243: 1110:Transcribed by RNA polymerase III 820:, which plays important roles in 9826: 9782: 9733: 9697: 9657: 9598: 9513: 9472: 9415: 9374: 9330: 9289: 9230: 9186: 9143: 9100: 9057: 9008: 8921: 8878: 8778: 8727: 8676: 8625: 8484: 8433: 8384: 8297: 8248: 8197: 8107: 8101: 8065: 8022: 8016: 7967: 7853: 7804: 7712: 7699: 7651: 7445: 7386: 7327: 7223: 7106: 7057: 7003: 6954: 6905: 6856: 5732:10.1128/MCB.21.22.7807-7816.2001 5575: 5427:Adelman K, Egan E (March 2017). 5233:Cancer Genetics and Cytogenetics 1646:) and homology-directed repair ( 1596:telomeric repeat-containing RNAs 1179:, these functions often involve 6797: 6745: 6704: 6603: 6562: 6425: 6374: 6325: 6282: 6233: 6188: 5905: 5756: 5707: 5612: 5569: 5518: 5469: 5420: 5363: 5306: 5223: 5174: 5118: 5079: 4932: 4823: 4723: 4590: 4541: 4492: 4449: 4398: 4349: 4252: 4217: 4166: 4117: 4066: 4017: 3959: 3910: 3807: 3758: 3706: 3657: 3606: 3557: 3508: 3457: 3359: 3310: 3259: 3221:NAR Genomics and Bioinformatics 3208: 3167: 3116: 3016: 2911: 2854: 2803: 2752: 2708: 2651: 2594: 2545: 2435: 1833:that encompassed a long ncRNA, 1819:single nucleotide polymorphisms 682: 8934:Molecular and Cellular Biology 7817:Molecular and Cellular Biology 7612:10.1126/science.344.6187.981-a 6979:10.1523/JNEUROSCI.0548-07.2007 6246:Molecular and Cellular Biology 5720:Molecular and Cellular Biology 2274: 2112: 2016: 1555:including H4 hypoacetylation, 1536:inactivation of a X-chromosome 1498:/Air in directing imprinting. 1195: 785:In gene-specific transcription 708:-specific adaptive selection. 655: 464:Plant, human, mouse, fly, worm 13: 1: 9498:10.1158/0008-5472.CAN-06-2004 9078:10.1161/CIRCRESAHA.115.303836 8848:(Database issue): D128–D134. 6730:10.1016/S0021-9258(18)54535-X 6351:10.1016/S0925-4773(02)00459-8 5782:10.1016/S1097-2765(03)00388-5 5245:10.1016/S0165-4608(01)00634-3 4730:Ponting CP, Haerty W (2022). 3582:10.1093/bioinformatics/btr209 3285:10.1093/bioinformatics/btz008 3278:(Database issue): D246–D251. 1956: 1908:, as identified for both the 1791:chronic lymphocytic leukaemia 1642:: nonhomologous end joining ( 1473: 9632:10.1371/journal.pone.0005027 8702:10.1371/journal.pgen.1004923 8651:10.1371/journal.pgen.1003423 7420:10.1371/journal.pone.0001182 7082:10.1016/j.molcel.2008.07.008 6616:Journal of Molecular Biology 6173:10.1016/j.molcel.2008.02.001 6132:10.1016/j.molcel.2007.12.013 5494:10.1016/j.celrep.2013.12.015 4957:10.1016/j.celrep.2014.05.023 4566:10.1016/j.bbagen.2013.10.035 4517:10.1016/j.celrep.2015.04.023 4192:10.1371/journal.pgen.1002841 1746:oral squamous cell carcinoma 1506:trimethylation of lysine 9 ( 1501:Almost all the genes at the 1218:internal ribosome entry site 739: 426:Human, fly, mouse, zebrafish 95: 7: 9121:10.1016/j.yjmcc.2018.11.004 6967:The Journal of Neuroscience 6918:The Journal of Cell Biology 6869:The Journal of Cell Biology 6761:The Journal of Neuroscience 4842:(Database issue): D168–73. 4793:(Database issue): D146–51. 3193:10.1016/j.ygeno.2022.110443 1919: 1685:tissues from patients with 922:NcRNAs also target general 10: 9929: 9583:10.1161/ATVBAHA.109.189522 9033:10.1007/s00439-021-02396-8 7529:10.1016/j.cell.2007.05.022 7472:10.1016/j.cell.2008.04.043 7066:"An inside job for siRNAs" 7013:Behavioural Brain Research 5331:10.1016/j.csbj.2023.09.027 3935:10.1016/j.cell.2013.06.009 3832:10.1016/j.cell.2011.10.002 3682:10.1016/j.cell.2015.01.009 3142:10.1186/s12864-024-10662-y 2137:10.1038/s41580-023-00612-z 1880:gene, a crucial enzyme in 1762:non-small cell lung cancer 1742:non-small cell lung cancer 1343:mobile transposon elements 1181:complementary base pairing 770:transcriptional regulation 9400:10.1007/s10038-006-0070-9 9387:Journal of Human Genetics 8370:10.1016/j.gde.2007.08.001 7992:10.1016/j.tig.2007.03.018 7035:10.1016/j.bbr.2004.02.015 6628:10.1016/j.jmb.2012.11.024 6538:10.1016/j.tig.2007.09.001 6338:Mechanisms of Development 5673:Nature Structural Biology 5291:10.1016/j.ccr.2007.07.027 4424:10.1186/s13059-016-0880-9 4374:10.1016/j.tig.2014.08.004 4238:10.1016/j.tig.2005.02.014 3632:10.1186/s13059-016-0880-9 2778:10.1186/s13059-016-0932-1 1583:Telomeric non-coding RNAs 1092:transcriptional activator 640:Evolutionary conservation 9707:Human Molecular Genetics 9526:Human Molecular Genetics 8505:10.1038/nchembio.2007.38 8409:10.1038/sj.emboj.7600071 8075:Human Molecular Genetics 6492:10.1126/stke.3552006pe40 6434:Molecular Carcinogenesis 5544:10.1186/1471-2164-11-614 4324:10.3389/fgene.2015.00002 4092:10.1186/gb-2013-14-5-r49 3483:10.1186/1471-2105-15-311 2025:"Visiting "noncodarnia"" 1837:. ANRIL is expressed in 1825:mapped to a long ncRNA, 1799:hepatocellular carcinoma 1767:hepatocellular carcinoma 1636:DNA double-strand breaks 1634:Incorrect reparation of 1365:In epigenetic regulation 1238:thyroid hormone receptor 799:RNA polymerase (RNAP) II 124:, but have little or no 9860:10.1073/pnas.1822046116 9448:10.1126/science.1142447 9264:10.1073/pnas.0500613102 8994:10.1089/dna.2006.25.135 8602:10.1126/science.1147182 8493:Nature Chemical Biology 8261:Genes & Development 8114:Genes & Development 7883:10.1126/science.1112009 7721:Journal of Cell Science 7585:10.1126/science.1117705 7199:10.1126/science.1157676 6668:Genes & Development 5104:10.1242/dev.129.19.4371 5043:Genes & Development 4648:Nature Reviews Genetics 4458:Nature Reviews Genetics 3783:10.1126/science.1248636 3025:Nature Reviews Genetics 2994:10.1126/science.1138341 2509:Genes & Development 2304:10.1126/science.1108625 2252:10.1126/science.1112014 2023:Perkel JM (June 2013). 1831:coronary artery disease 1510:) and 27 of histone 3 ( 1421:Hox regulatory elements 1351:RISC effector complexes 944:dihydrofolate reductase 875:binds and inhibits the 873:RNA binding protein TLS 834:ultra-conserved element 545:Support vector machine 513:Support vector machine 257:Main model / algorithm 235:Identification software 53:, generally defined as 9359:10.1074/jbc.M501704200 9208:10.1038/sj.onc.1207880 9164:10.1038/sj.onc.1209846 8887:Neurochemical Research 8842:Nucleic Acids Research 8753:10.1261/rna.073114.119 8041:10.1101/sqb.2004.69.55 7829:10.1128/MCB.18.10.5634 7664:Nucleic Acids Research 7232:Developmental Dynamics 6881:10.1083/jcb.141.7.1601 6831:10.1073/pnas.88.6.2093 6588:10.1074/jbc.M700079200 6156:"Modular RNA heats up" 5930:10.1093/nar/23.10.1758 5918:Nucleic Acids Research 5625:Nucleic Acids Research 4888:Nucleic Acids Research 4836:Nucleic Acids Research 4787:Nucleic Acids Research 3521:Nucleic Acids Research 3421:Nucleic Acids Research 3372:Nucleic Acids Research 3323:Nucleic Acids Research 2924:Nucleic Acids Research 2867:Nucleic Acids Research 2664:Nucleic Acids Research 1856:The complexity of the 1787:ultraconserved regions 1628:monoallelic expression 1278:central nervous system 71:small interfering RNAs 35: 7635:|...}} 7606:(Retracted, see 7361:10.1073/pnas.86.1.177 6930:10.1083/jcb.200506006 5637:10.1093/nar/15.3.1047 4311:Frontiers in Genetics 4142:10.1101/gr.165035.113 3234:10.1093/nargab/lqz024 2411:10.1101/gr.132159.111 1823:myocardial infarction 1565:H4K20 monomethylation 1563:hypermethylation and 1116:transcription factors 924:transcription factors 849:and to contribute to 816:transcription factor 403:Relationship between 75:Piwi-interacting RNAs 33: 9066:Circulation Research 8982:DNA and Cell Biology 8946:10.1128/MCB.7.9.3324 8804:10.3390/biom11040550 8322:10.1093/emboj/cdf655 8087:10.1093/hmg/8.7.1209 7727:(Pt 16): 2755–2761. 6258:10.1128/MCB.02263-07 4273:10.1038/nsmb0207-103 2829:10.3390/ncrna7020036 2521:10.1101/gad.17446611 2192:10.1038/nrm.2017.104 1991:10.3390/ncrna5010017 1914:yellow fever vaccine 1795:colorectal carcinoma 1683:post-mortem interval 1679:neurological disease 1668:neurological disease 1654:In aging and disease 1626:, ASARs show random 1557:H3K27 trimethylation 1459:protein-coding genes 1404:DNA demethylase TET2 1138:ncRNA genes such as 1061:, the expression of 996:repetitive sequences 889:RNA-binding proteins 877:CREB binding protein 836:located between the 806:transcription factor 734:secondary structures 678:biological function. 198:Genomic organization 79:small nucleolar RNAs 39:Long non-coding RNAs 9851:2019PNAS..11617121D 9845:(34): 17121–17126. 9623:2009PLoSO...4.5027L 9440:2007Sci...316.1488M 9434:(5830): 1488–1491. 9352:(25): 24159–24167. 9255:2005PNAS..102.3627E 8593:2007Sci...318..798A 8531:Nature Cell Biology 8454:1998Natur.393..599C 8218:2002Natur.415..810S 8126:10.1101/gad.1416906 7943:10.1038/nature06468 7935:2008Natur.451..202Y 7875:2005Sci...309.1564R 7869:(5740): 1564–1566. 7780:10.1098/rsob.200126 7676:10.1093/nar/gkaa097 7577:2006Sci...311.1118S 7571:(5764): 1118–1123. 7411:2007PLoSO...2.1182R 7352:1989PNAS...86..177N 7303:10.1038/nature06008 7295:2007Natur.448..553M 7191:2008Sci...320.1336O 7185:(5881): 1336–1341. 7139:10.1038/nature07007 7131:2008Natur.453..798C 6822:1991PNAS...88.2093T 6723:(33): 22083–22086. 6395:1985Natur.314..553S 5890:10.1038/nature01262 5881:2002Natur.420..520W 5822:2001Natur.409..860L 5590:10.1038/nature05519 5445:2017Natur.543..183A 5396:10.1038/nature06992 5388:2008Natur.454..126W 5152:10.1038/nature05295 5144:2006Natur.444..499P 5055:10.1101/gad.1416106 4900:10.1093/nar/gkab998 4799:10.1093/nar/gkq1138 4708:10.1093/bfgp/elp038 4470:10.1038/nrg.2016.85 3993:10.1038/nature07672 3985:2009Natur.458..223G 3885:10.7554/eLife.08890 3736:10.1038/nature21034 3728:2017Natur.541..228M 3533:10.1093/nar/gkw1306 3092:10.1038/nature05874 3084:2007Natur.447..799B 2986:2007Sci...316.1484K 2980:(5830): 1484–1488. 2936:10.1093/nar/gkv1215 2879:10.1093/nar/gkac999 2676:10.1093/nar/gkaa850 2619:2016NatSR...632753Y 2469:10.1038/nature21374 2461:2017Natur.543..199H 2358:10.1038/nature12943 2350:2014Natur.505..635N 2296:2005Sci...308.1149C 2290:(5725): 1149–1154. 2244:2005Sci...309.1559F 2238:(5740): 1559–1563. 1882:Alzheimer's disease 1808:malignant processes 1687:Alzheimer's disease 1548:embryonic stem cell 1524:histone methylation 1402:and recruitment of 1379:histone acetylation 1314:double-stranded RNA 1312:, the formation of 1270:synaptic plasticity 1043:repetitive elements 447:Logistic regression 208:sense and antisense 162:developmental stage 9719:10.1093/hmg/ddh245 9539:10.1093/hmg/ddm352 8899:10.1007/bf00968788 8854:10.1093/nar/gky960 8273:10.1101/gad.206201 7980:Trends in Genetics 7733:10.1242/jcs.007633 7244:10.1002/dvdy.21094 6680:10.1101/gad.455708 6526:Trends in Genetics 6219:10.1002/bies.10332 6071:10.1261/rna.310307 5199:10.1038/ng.2007.55 4848:10.1093/nar/gku988 4615:10.1038/nmeth.4066 4362:Trends in Genetics 4226:Trends in Genetics 4042:10.1101/gr.6036807 3470:BMC Bioinformatics 3433:10.1093/nar/gkt646 3384:10.1093/nar/gkw798 3335:10.1093/nar/gkt006 2607:Scientific Reports 2570:10.1101/gr.4200206 2393:(September 2012). 1728:growth in several 1716:. For example, in 1697:transcript of the 1520:Polycomb complexes 1230:ectopic expression 1122:itself (including 1096:regulatory circuit 932:initiation complex 762:community curation 689:conserved sequence 670:Ribosome profiling 286:PLEKv2 source code 126:open reading frame 36: 18:Long noncoding RNA 9713:(19): 2221–2231. 9673:(14): 1147–1149. 9576:(10): 1671–1677. 9393:(12): 1087–1099. 9249:(10): 3627–3632. 9202:(39): 6684–6692. 8587:(5851): 798–801. 8448:(6685): 599–601. 8316:(23): 6560–6570. 8267:(18): 2361–2366. 8212:(6873): 810–813. 8169:(12): 1296–1300. 8120:(10): 1268–1282. 7929:(7175): 202–206. 7823:(10): 5634–5642. 7289:(7153): 553–560. 7125:(7196): 798–802. 6973:(33): 8885–8892. 6622:(19): 3723–3730. 6581:(12): 8883–8894. 6389:(6011): 553–556. 6252:(11): 3713–3728. 5972:(12): 1282–1290. 5924:(10): 1758–1765. 5875:(6915): 520–562. 5816:(6822): 860–921. 5726:(22): 7807–7816. 5584:(7128): 666–670. 5439:(7644): 183–185. 5382:(7200): 126–130. 5138:(7118): 499–502. 5098:(19): 4371–4386. 5049:(11): 1470–1484. 4894:(D1): D190–D195. 3979:(7235): 223–227. 3777:(6172): 1248636. 3722:(7636): 228–232. 3576:(13): i275–i282. 3078:(7146): 799–816. 2873:(D1): D186–D191. 2730:10.1038/nsmb.2660 2670:(D1): D962–D968. 2627:10.1038/srep32753 2515:(18): 1915–1927. 2455:(7644): 199–204. 2344:(7485): 635–640. 2088:10.4161/rna.24604 2042:10.2144/000114037 2035:(6): 301, 303–4. 1910:influenza vaccine 1750:colorectal cancer 1540:placental mammals 1320:(endo-siRNAs) in 1228:. Therefore, the 1216:that contains an 1152:sequence homology 934:that assemble on 926:required for the 897:Apolipoprotein A1 795:RNA transcription 653: 652: 529:Vertebrate, Plant 164:specificity, and 102:complementary DNA 16:(Redirected from 9920: 9883: 9882: 9872: 9862: 9830: 9824: 9823: 9786: 9780: 9779: 9769: 9737: 9731: 9730: 9701: 9695: 9694: 9685: 10987042. 9661: 9655: 9654: 9644: 9634: 9602: 9596: 9595: 9585: 9561: 9552: 9551: 9541: 9517: 9511: 9510: 9500: 9491:(8): 3963–3969. 9476: 9470: 9469: 9459: 9419: 9413: 9412: 9402: 9378: 9372: 9371: 9361: 9343: 9334: 9328: 9327: 9317: 9308:(4): 1297–1305. 9293: 9287: 9286: 9276: 9266: 9234: 9228: 9227: 9190: 9184: 9183: 9147: 9141: 9140: 9104: 9098: 9097: 9061: 9055: 9054: 9044: 9012: 9006: 9005: 8977: 8968: 8967: 8957: 8940:(9): 3324–3327. 8925: 8919: 8918: 8882: 8876: 8875: 8865: 8833: 8827: 8826: 8816: 8806: 8782: 8776: 8775: 8765: 8755: 8731: 8725: 8724: 8714: 8704: 8680: 8674: 8673: 8663: 8653: 8629: 8623: 8622: 8604: 8572: 8563: 8562: 8526: 8517: 8516: 8488: 8482: 8481: 8437: 8431: 8430: 8420: 8397:The EMBO Journal 8388: 8382: 8381: 8353: 8344: 8343: 8333: 8310:The EMBO Journal 8301: 8295: 8294: 8284: 8252: 8246: 8245: 8201: 8195: 8194: 8157: 8148: 8147: 8137: 8105: 8099: 8098: 8081:(7): 1209–1217. 8069: 8063: 8062: 8052: 8020: 8014: 8013: 8003: 7971: 7965: 7964: 7954: 7914: 7903: 7902: 7857: 7851: 7850: 7840: 7808: 7802: 7801: 7791: 7759: 7753: 7752: 7716: 7710: 7703: 7697: 7687: 7670:(7): 3935–3948. 7655: 7649: 7648: 7646: 7644: 7636: 7625:Retraction Watch 7604: 7560: 7551: 7550: 7540: 7523:(7): 1311–1323. 7504: 7493: 7492: 7474: 7465:(6): 1106–1117. 7449: 7443: 7442: 7432: 7422: 7390: 7384: 7383: 7373: 7363: 7331: 7325: 7324: 7314: 7273: 7264: 7263: 7238:(4): 1144–1156. 7227: 7221: 7220: 7210: 7170: 7161: 7160: 7150: 7110: 7104: 7103: 7093: 7061: 7055: 7054: 7028: 7007: 7001: 7000: 6990: 6958: 6952: 6951: 6941: 6909: 6903: 6902: 6892: 6875:(7): 1601–1611. 6860: 6854: 6853: 6843: 6833: 6816:(6): 2093–2097. 6801: 6795: 6794: 6784: 6767:(6): 2382–2390. 6749: 6743: 6742: 6732: 6708: 6702: 6701: 6691: 6659: 6650: 6649: 6639: 6607: 6601: 6600: 6590: 6566: 6560: 6559: 6549: 6521: 6512: 6511: 6475: 6466: 6465: 6446:10.1002/mc.20057 6429: 6423: 6422: 6403:10.1038/314553a0 6378: 6372: 6371: 6353: 6329: 6323: 6322: 6286: 6280: 6279: 6269: 6237: 6231: 6230: 6212: 6192: 6186: 6185: 6175: 6151: 6145: 6144: 6134: 6110: 6093: 6092: 6082: 6050: 6044: 6043: 6007: 5998: 5997: 5961: 5952: 5951: 5941: 5909: 5903: 5902: 5892: 5860: 5854: 5853: 5843: 5833: 5831:10.1038/35057062 5801: 5795: 5794: 5784: 5760: 5754: 5753: 5743: 5711: 5705: 5704: 5668: 5659: 5658: 5648: 5631:(3): 1047–1061. 5616: 5610: 5609: 5573: 5567: 5566: 5556: 5546: 5522: 5516: 5515: 5505: 5473: 5467: 5466: 5456: 5424: 5418: 5417: 5407: 5367: 5361: 5360: 5350: 5310: 5304: 5303: 5293: 5268: 5257: 5256: 5227: 5221: 5220: 5210: 5178: 5172: 5171: 5122: 5116: 5115: 5083: 5077: 5076: 5066: 5034: 5025: 5024: 4988: 4979: 4978: 4968: 4951:(6): 1858–1866. 4936: 4930: 4929: 4919: 4879: 4870: 4869: 4859: 4827: 4821: 4820: 4810: 4778: 4772: 4771: 4761: 4751: 4727: 4721: 4720: 4710: 4686: 4680: 4679: 4643: 4637: 4636: 4626: 4594: 4588: 4587: 4577: 4560:(3): 1063–1071. 4545: 4539: 4538: 4528: 4511:(7): 1110–1122. 4496: 4490: 4489: 4453: 4447: 4446: 4436: 4426: 4402: 4396: 4395: 4385: 4353: 4347: 4346: 4336: 4326: 4302: 4293: 4292: 4256: 4250: 4249: 4221: 4215: 4214: 4204: 4194: 4170: 4164: 4163: 4153: 4121: 4115: 4114: 4104: 4094: 4070: 4064: 4063: 4053: 4021: 4015: 4014: 4004: 3963: 3957: 3956: 3946: 3914: 3908: 3907: 3897: 3887: 3863: 3854: 3853: 3843: 3811: 3805: 3804: 3794: 3762: 3756: 3755: 3710: 3704: 3703: 3693: 3661: 3655: 3654: 3644: 3634: 3610: 3604: 3603: 3593: 3561: 3555: 3554: 3544: 3512: 3506: 3505: 3495: 3485: 3461: 3455: 3454: 3444: 3412: 3406: 3405: 3395: 3363: 3357: 3356: 3346: 3314: 3308: 3307: 3297: 3287: 3263: 3257: 3256: 3246: 3236: 3212: 3206: 3205: 3195: 3171: 3165: 3164: 3154: 3144: 3120: 3114: 3113: 3103: 3063: 3057: 3056: 3020: 3014: 3013: 2964: 2958: 2957: 2947: 2915: 2909: 2908: 2898: 2858: 2852: 2851: 2841: 2831: 2807: 2801: 2800: 2790: 2780: 2756: 2750: 2749: 2724:(9): 1131–1139. 2712: 2706: 2705: 2695: 2655: 2649: 2648: 2638: 2598: 2592: 2591: 2581: 2549: 2543: 2542: 2532: 2500: 2491: 2490: 2480: 2439: 2433: 2432: 2422: 2405:(9): 1775–1789. 2389: 2378: 2377: 2333: 2324: 2323: 2278: 2272: 2271: 2227: 2214: 2213: 2203: 2171: 2165: 2164: 2116: 2110: 2109: 2099: 2067: 2058: 2057: 2044: 2020: 2014: 2013: 2003: 1993: 1969: 1718:prostate tumours 1640:eukaryotic cells 1208:it encodes. The 1088:heat shock genes 1080:heat shock RNA-1 824:development and 239: 238: 122:poly-adenylation 49:) are a type of 21: 9928: 9927: 9923: 9922: 9921: 9919: 9918: 9917: 9888: 9887: 9886: 9831: 9827: 9792:Nature Genetics 9787: 9783: 9746:Nature Medicine 9738: 9734: 9702: 9698: 9662: 9658: 9603: 9599: 9562: 9555: 9518: 9514: 9485:Cancer Research 9477: 9473: 9420: 9416: 9379: 9375: 9341: 9335: 9331: 9294: 9290: 9235: 9231: 9191: 9187: 9148: 9144: 9105: 9101: 9062: 9058: 9013: 9009: 8978: 8971: 8926: 8922: 8883: 8879: 8834: 8830: 8783: 8779: 8732: 8728: 8695:(1): e1004923. 8681: 8677: 8644:(4): e1003423. 8630: 8626: 8573: 8566: 8543:10.1038/ncb1685 8527: 8520: 8499:(10): 640–649. 8489: 8485: 8438: 8434: 8389: 8385: 8354: 8347: 8302: 8298: 8253: 8249: 8226:10.1038/415810a 8202: 8198: 8163:Nature Genetics 8158: 8151: 8106: 8102: 8070: 8066: 8021: 8017: 7972: 7968: 7915: 7906: 7858: 7854: 7809: 7805: 7760: 7756: 7717: 7713: 7656: 7652: 7638: 7630: 7628: 7605: 7561: 7554: 7505: 7496: 7450: 7446: 7391: 7387: 7332: 7328: 7274: 7267: 7228: 7224: 7171: 7164: 7111: 7107: 7062: 7058: 7026:10.1.1.572.8071 7008: 7004: 6959: 6955: 6910: 6906: 6861: 6857: 6802: 6798: 6750: 6746: 6709: 6705: 6660: 6653: 6608: 6604: 6567: 6563: 6532:(12): 614–622. 6522: 6515: 6476: 6469: 6430: 6426: 6379: 6375: 6330: 6326: 6291:Nature Genetics 6287: 6283: 6238: 6234: 6210:10.1.1.476.7561 6203:(10): 930–939. 6193: 6189: 6152: 6148: 6111: 6096: 6051: 6047: 6024:10.1038/nsmb812 6008: 6001: 5966:Nature Genetics 5962: 5955: 5910: 5906: 5861: 5857: 5802: 5798: 5761: 5757: 5712: 5708: 5679:(11): 800–805. 5669: 5662: 5617: 5613: 5574: 5570: 5523: 5519: 5474: 5470: 5454:10.1038/543183a 5425: 5421: 5368: 5364: 5311: 5307: 5269: 5260: 5228: 5224: 5187:Nature Genetics 5179: 5175: 5123: 5119: 5084: 5080: 5035: 5028: 5005:10.1038/nrm1946 4989: 4982: 4937: 4933: 4880: 4873: 4828: 4824: 4779: 4775: 4728: 4724: 4687: 4683: 4660:10.1038/nrg2521 4644: 4640: 4595: 4591: 4546: 4542: 4497: 4493: 4464:(10): 601–614. 4454: 4450: 4403: 4399: 4368:(10): 439–452. 4354: 4350: 4303: 4296: 4257: 4253: 4222: 4218: 4185:(7): e1002841. 4171: 4167: 4130:Genome Research 4122: 4118: 4071: 4067: 4030:Genome Research 4022: 4018: 3964: 3960: 3915: 3911: 3864: 3857: 3812: 3808: 3763: 3759: 3711: 3707: 3662: 3658: 3611: 3607: 3562: 3558: 3513: 3509: 3462: 3458: 3413: 3409: 3364: 3360: 3315: 3311: 3264: 3260: 3213: 3209: 3172: 3168: 3121: 3117: 3064: 3060: 3037:10.1038/nrg2083 3021: 3017: 2965: 2961: 2930:(D1): D1161–6. 2916: 2912: 2859: 2855: 2808: 2804: 2757: 2753: 2713: 2709: 2656: 2652: 2599: 2595: 2558:Genome Research 2550: 2546: 2501: 2494: 2440: 2436: 2399:Genome Research 2390: 2381: 2334: 2327: 2279: 2275: 2228: 2217: 2172: 2168: 2117: 2113: 2068: 2061: 2021: 2017: 1970: 1963: 1959: 1922: 1902:immune response 1891:DNA methylation 1847:atherosclerosis 1760:of early-stage 1734:prostate cancer 1693:brain-specific 1656: 1612:DNA replication 1608: 1585: 1532: 1476: 1442:gene expression 1375:DNA methylation 1367: 1306: 1246: 1198: 1186:gene expression 1169:mRNA processing 1165: 1112: 1100:gene expression 1067:viral infection 1057:In addition to 1014:and ~6% of the 989:gene expression 984:phosphorylating 920: 903:modifications. 866:gene expression 787: 782: 742: 685: 658: 400:FASTA, BED, GTF 317:DeepPlnc Server 245:Taxonomic group 237: 200: 98: 63:non-coding RNAs 28: 23: 22: 15: 12: 11: 5: 9926: 9916: 9915: 9910: 9908:Non-coding RNA 9905: 9900: 9885: 9884: 9825: 9804:10.1038/ng1157 9798:(2): 157–165. 9781: 9758:10.1038/nm1784 9752:(7): 723–730. 9732: 9696: 9656: 9597: 9553: 9532:(6): 806–814. 9512: 9471: 9414: 9373: 9329: 9288: 9229: 9185: 9158:(6): 851–858. 9142: 9099: 9072:(7): 668–677. 9056: 9021:Human Genetics 9007: 8988:(3): 135–141. 8969: 8920: 8893:(6): 591–597. 8877: 8828: 8777: 8746:(6): 724–738. 8726: 8675: 8624: 8564: 8537:(2): 228–236. 8518: 8483: 8432: 8403:(3): 594–604. 8383: 8364:(5): 387–393. 8345: 8296: 8247: 8196: 8175:10.1038/ng1467 8149: 8100: 8064: 8015: 7986:(6): 284–292. 7966: 7904: 7852: 7803: 7754: 7711: 7650: 7552: 7494: 7444: 7385: 7346:(1): 177–181. 7326: 7265: 7222: 7162: 7105: 7076:(3): 309–312. 7070:Molecular Cell 7056: 7019:(1): 273–289. 7002: 6953: 6924:(5): 811–821. 6904: 6855: 6796: 6744: 6703: 6674:(6): 756–769. 6651: 6602: 6561: 6513: 6480:Science's STKE 6467: 6424: 6373: 6344:(4): 503–509. 6324: 6297:(2): 167–174. 6281: 6232: 6187: 6166:(4): 415–417. 6160:Molecular Cell 6146: 6125:(4): 499–509. 6119:Molecular Cell 6094: 6065:(4): 583–596. 6045: 6018:(9): 822–829. 5999: 5978:10.1038/ng1478 5953: 5904: 5855: 5796: 5775:(4): 971–982. 5769:Molecular Cell 5755: 5706: 5685:10.1038/nsb862 5660: 5611: 5568: 5517: 5488:(1): 222–230. 5468: 5419: 5362: 5305: 5284:(3): 215–229. 5258: 5222: 5193:(2): 158–160. 5173: 5117: 5078: 5026: 4999:(8): 612–616. 4980: 4931: 4871: 4822: 4773: 4722: 4701:(6): 407–423. 4681: 4654:(3): 155–159. 4638: 4603:Nature Methods 4589: 4540: 4491: 4448: 4411:Genome Biology 4397: 4348: 4294: 4267:(2): 103–105. 4251: 4232:(5): 287–288. 4216: 4165: 4136:(4): 616–628. 4116: 4079:Genome Biology 4065: 4036:(5): 556–565. 4016: 3958: 3929:(1): 240–251. 3909: 3855: 3826:(4): 789–802. 3806: 3757: 3705: 3676:(4): 595–606. 3656: 3619:Genome Biology 3605: 3570:Bioinformatics 3556: 3507: 3456: 3407: 3358: 3309: 3272:Bioinformatics 3258: 3207: 3166: 3115: 3058: 3031:(6): 413–423. 3015: 2959: 2910: 2853: 2816:Non-Coding RNA 2802: 2765:Genome Biology 2751: 2707: 2650: 2593: 2544: 2492: 2434: 2379: 2325: 2273: 2215: 2186:(3): 143–157. 2166: 2131:(9): 601–602. 2111: 2082:(6): 925–933. 2059: 2015: 1978:Non-Coding RNA 1960: 1958: 1955: 1954: 1953: 1948: 1943: 1938: 1933: 1928: 1921: 1918: 1897:in a patient. 1771:tumourigenesis 1655: 1652: 1607: 1604: 1584: 1581: 1531: 1528: 1475: 1472: 1430:RNA polymerase 1366: 1363: 1305: 1302: 1282:synaptogenesis 1245: 1244:In translation 1242: 1197: 1194: 1164: 1161: 1111: 1108: 919: 916: 908:X-inactivation 830:Sonic hedgehog 786: 783: 781: 778: 741: 738: 684: 681: 657: 654: 651: 650: 648: 645: 642: 637: 634: 627: 624: 621: 617: 616: 614: 611: 608: 602: 599: 597: 594: 591: 587: 586: 584: 581: 578: 577:Random forest 575: 572: 565: 562: 559: 555: 554: 552: 549: 546: 543: 540: 533: 530: 527: 523: 522: 520: 517: 514: 511: 508: 506: 503: 500: 496: 495: 493: 490: 487: 482: 479: 472: 465: 462: 458: 457: 455: 452: 449: 444: 441: 434: 427: 424: 420: 419: 417: 414: 411: 401: 398: 396: 389: 386: 382: 381: 379: 376: 373: 371:Neural network 368: 365: 358: 351: 348: 344: 343: 341: 338: 335: 333:Neural network 330: 327: 320: 313: 310: 306: 305: 303: 300: 297: 292: 289: 282: 275: 274:Plant, animal 272: 268: 267: 264: 263:Year published 261: 258: 255: 252: 249: 246: 243: 236: 233: 199: 196: 143:neural tissues 130:polyadenylated 110:messenger RNAs 97: 94: 57:more than 200 26: 9: 6: 4: 3: 2: 9925: 9914: 9913:Biotechnology 9911: 9909: 9906: 9904: 9901: 9899: 9896: 9895: 9893: 9880: 9876: 9871: 9866: 9861: 9856: 9852: 9848: 9844: 9840: 9836: 9829: 9821: 9817: 9813: 9809: 9805: 9801: 9797: 9793: 9785: 9777: 9773: 9768: 9763: 9759: 9755: 9751: 9747: 9743: 9736: 9728: 9724: 9720: 9716: 9712: 9708: 9700: 9692: 9688: 9684: 9680: 9676: 9672: 9668: 9660: 9652: 9648: 9643: 9638: 9633: 9628: 9624: 9620: 9616: 9612: 9608: 9601: 9593: 9589: 9584: 9579: 9575: 9571: 9567: 9560: 9558: 9549: 9545: 9540: 9535: 9531: 9527: 9523: 9516: 9508: 9504: 9499: 9494: 9490: 9486: 9482: 9475: 9467: 9463: 9458: 9453: 9449: 9445: 9441: 9437: 9433: 9429: 9425: 9418: 9410: 9406: 9401: 9396: 9392: 9388: 9384: 9377: 9369: 9365: 9360: 9355: 9351: 9347: 9340: 9333: 9325: 9321: 9316: 9311: 9307: 9303: 9299: 9292: 9284: 9280: 9275: 9270: 9265: 9260: 9256: 9252: 9248: 9244: 9240: 9233: 9225: 9221: 9217: 9213: 9209: 9205: 9201: 9197: 9189: 9181: 9177: 9173: 9169: 9165: 9161: 9157: 9153: 9146: 9138: 9134: 9130: 9126: 9122: 9118: 9114: 9110: 9103: 9095: 9091: 9087: 9083: 9079: 9075: 9071: 9067: 9060: 9052: 9048: 9043: 9038: 9034: 9030: 9026: 9022: 9018: 9011: 9003: 8999: 8995: 8991: 8987: 8983: 8976: 8974: 8965: 8961: 8956: 8951: 8947: 8943: 8939: 8935: 8931: 8924: 8916: 8912: 8908: 8904: 8900: 8896: 8892: 8888: 8881: 8873: 8869: 8864: 8859: 8855: 8851: 8847: 8843: 8839: 8832: 8824: 8820: 8815: 8810: 8805: 8800: 8796: 8792: 8788: 8781: 8773: 8769: 8764: 8759: 8754: 8749: 8745: 8741: 8737: 8730: 8722: 8718: 8713: 8708: 8703: 8698: 8694: 8690: 8689:PLOS Genetics 8686: 8679: 8671: 8667: 8662: 8657: 8652: 8647: 8643: 8639: 8638:PLOS Genetics 8635: 8628: 8620: 8616: 8612: 8608: 8603: 8598: 8594: 8590: 8586: 8582: 8578: 8571: 8569: 8560: 8556: 8552: 8548: 8544: 8540: 8536: 8532: 8525: 8523: 8514: 8510: 8506: 8502: 8498: 8494: 8487: 8479: 8475: 8471: 8467: 8463: 8462:10.1038/31275 8459: 8455: 8451: 8447: 8443: 8436: 8428: 8424: 8419: 8414: 8410: 8406: 8402: 8398: 8394: 8387: 8379: 8375: 8371: 8367: 8363: 8359: 8352: 8350: 8341: 8337: 8332: 8327: 8323: 8319: 8315: 8311: 8307: 8300: 8292: 8288: 8283: 8278: 8274: 8270: 8266: 8262: 8258: 8251: 8243: 8239: 8235: 8231: 8227: 8223: 8219: 8215: 8211: 8207: 8200: 8192: 8188: 8184: 8180: 8176: 8172: 8168: 8164: 8156: 8154: 8145: 8141: 8136: 8131: 8127: 8123: 8119: 8115: 8111: 8104: 8096: 8092: 8088: 8084: 8080: 8076: 8068: 8060: 8056: 8051: 8046: 8042: 8038: 8034: 8030: 8026: 8019: 8011: 8007: 8002: 7997: 7993: 7989: 7985: 7981: 7977: 7970: 7962: 7958: 7953: 7948: 7944: 7940: 7936: 7932: 7928: 7924: 7920: 7913: 7911: 7909: 7900: 7896: 7892: 7888: 7884: 7880: 7876: 7872: 7868: 7864: 7856: 7848: 7844: 7839: 7834: 7830: 7826: 7822: 7818: 7814: 7807: 7799: 7795: 7790: 7785: 7781: 7777: 7774:(9): 200126. 7773: 7769: 7765: 7758: 7750: 7746: 7742: 7738: 7734: 7730: 7726: 7722: 7715: 7709: 7707: 7702: 7695: 7691: 7686: 7681: 7677: 7673: 7669: 7665: 7661: 7654: 7642: 7634: 7627: 7626: 7621: 7617: 7613: 7609: 7602: 7598: 7594: 7590: 7586: 7582: 7578: 7574: 7570: 7566: 7559: 7557: 7548: 7544: 7539: 7534: 7530: 7526: 7522: 7518: 7514: 7511:(June 2007). 7510: 7503: 7501: 7499: 7490: 7486: 7482: 7478: 7473: 7468: 7464: 7460: 7456: 7448: 7440: 7436: 7431: 7426: 7421: 7416: 7412: 7408: 7405:(11): e1182. 7404: 7400: 7396: 7389: 7381: 7377: 7372: 7367: 7362: 7357: 7353: 7349: 7345: 7341: 7337: 7330: 7322: 7318: 7313: 7308: 7304: 7300: 7296: 7292: 7288: 7284: 7280: 7272: 7270: 7261: 7257: 7253: 7249: 7245: 7241: 7237: 7233: 7226: 7218: 7214: 7209: 7204: 7200: 7196: 7192: 7188: 7184: 7180: 7176: 7169: 7167: 7158: 7154: 7149: 7144: 7140: 7136: 7132: 7128: 7124: 7120: 7116: 7109: 7101: 7097: 7092: 7087: 7083: 7079: 7075: 7071: 7067: 7060: 7052: 7048: 7044: 7040: 7036: 7032: 7027: 7022: 7018: 7014: 7006: 6998: 6994: 6989: 6984: 6980: 6976: 6972: 6968: 6964: 6957: 6949: 6945: 6940: 6935: 6931: 6927: 6923: 6919: 6915: 6908: 6900: 6896: 6891: 6886: 6882: 6878: 6874: 6870: 6866: 6859: 6851: 6847: 6842: 6837: 6832: 6827: 6823: 6819: 6815: 6811: 6807: 6800: 6792: 6788: 6783: 6778: 6774: 6770: 6766: 6762: 6758: 6754: 6748: 6740: 6736: 6731: 6726: 6722: 6718: 6714: 6707: 6699: 6695: 6690: 6685: 6681: 6677: 6673: 6669: 6665: 6658: 6656: 6647: 6643: 6638: 6633: 6629: 6625: 6621: 6617: 6613: 6606: 6598: 6594: 6589: 6584: 6580: 6576: 6572: 6565: 6557: 6553: 6548: 6547:11381/1706964 6543: 6539: 6535: 6531: 6527: 6520: 6518: 6509: 6505: 6501: 6497: 6493: 6489: 6486:(355): pe40. 6485: 6481: 6474: 6472: 6463: 6459: 6455: 6451: 6447: 6443: 6439: 6435: 6428: 6420: 6416: 6412: 6408: 6404: 6400: 6396: 6392: 6388: 6384: 6377: 6369: 6365: 6361: 6357: 6352: 6347: 6343: 6339: 6335: 6328: 6320: 6316: 6312: 6308: 6304: 6303:10.1038/ng820 6300: 6296: 6292: 6285: 6277: 6273: 6268: 6263: 6259: 6255: 6251: 6247: 6243: 6236: 6228: 6224: 6220: 6216: 6211: 6206: 6202: 6198: 6191: 6183: 6179: 6174: 6169: 6165: 6161: 6157: 6150: 6142: 6138: 6133: 6128: 6124: 6120: 6116: 6109: 6107: 6105: 6103: 6101: 6099: 6090: 6086: 6081: 6076: 6072: 6068: 6064: 6060: 6056: 6049: 6041: 6037: 6033: 6029: 6025: 6021: 6017: 6013: 6006: 6004: 5995: 5991: 5987: 5983: 5979: 5975: 5971: 5967: 5960: 5958: 5949: 5945: 5940: 5935: 5931: 5927: 5923: 5919: 5915: 5908: 5900: 5896: 5891: 5886: 5882: 5878: 5874: 5870: 5866: 5859: 5851: 5847: 5842: 5841:2027.42/62798 5837: 5832: 5827: 5823: 5819: 5815: 5811: 5807: 5800: 5792: 5788: 5783: 5778: 5774: 5770: 5766: 5759: 5751: 5747: 5742: 5737: 5733: 5729: 5725: 5721: 5717: 5710: 5702: 5698: 5694: 5690: 5686: 5682: 5678: 5674: 5667: 5665: 5656: 5652: 5647: 5642: 5638: 5634: 5630: 5626: 5622: 5615: 5607: 5603: 5599: 5595: 5591: 5587: 5583: 5579: 5572: 5564: 5560: 5555: 5550: 5545: 5540: 5536: 5532: 5528: 5521: 5513: 5509: 5504: 5499: 5495: 5491: 5487: 5483: 5479: 5472: 5464: 5460: 5455: 5450: 5446: 5442: 5438: 5434: 5430: 5423: 5415: 5411: 5406: 5401: 5397: 5393: 5389: 5385: 5381: 5377: 5373: 5366: 5358: 5354: 5349: 5344: 5340: 5336: 5332: 5328: 5325:: 4887–4894. 5324: 5320: 5316: 5309: 5301: 5297: 5292: 5287: 5283: 5279: 5275: 5267: 5265: 5263: 5254: 5250: 5246: 5242: 5238: 5234: 5226: 5218: 5214: 5209: 5204: 5200: 5196: 5192: 5188: 5184: 5177: 5169: 5165: 5161: 5157: 5153: 5149: 5145: 5141: 5137: 5133: 5129: 5121: 5113: 5109: 5105: 5101: 5097: 5093: 5089: 5082: 5074: 5070: 5065: 5060: 5056: 5052: 5048: 5044: 5040: 5033: 5031: 5022: 5018: 5014: 5010: 5006: 5002: 4998: 4994: 4987: 4985: 4976: 4972: 4967: 4962: 4958: 4954: 4950: 4946: 4942: 4935: 4927: 4923: 4918: 4913: 4909: 4905: 4901: 4897: 4893: 4889: 4885: 4878: 4876: 4867: 4863: 4858: 4853: 4849: 4845: 4841: 4837: 4833: 4826: 4818: 4814: 4809: 4804: 4800: 4796: 4792: 4788: 4784: 4777: 4769: 4765: 4760: 4755: 4750: 4745: 4741: 4737: 4733: 4726: 4718: 4714: 4709: 4704: 4700: 4696: 4692: 4685: 4677: 4673: 4669: 4665: 4661: 4657: 4653: 4649: 4642: 4634: 4630: 4625: 4620: 4616: 4612: 4608: 4604: 4600: 4593: 4585: 4581: 4576: 4571: 4567: 4563: 4559: 4555: 4551: 4544: 4536: 4532: 4527: 4522: 4518: 4514: 4510: 4506: 4502: 4495: 4487: 4483: 4479: 4475: 4471: 4467: 4463: 4459: 4452: 4444: 4440: 4435: 4430: 4425: 4420: 4416: 4412: 4408: 4401: 4393: 4389: 4384: 4379: 4375: 4371: 4367: 4363: 4359: 4352: 4344: 4340: 4335: 4330: 4325: 4320: 4316: 4312: 4308: 4301: 4299: 4290: 4286: 4282: 4278: 4274: 4270: 4266: 4262: 4255: 4247: 4243: 4239: 4235: 4231: 4227: 4220: 4212: 4208: 4203: 4198: 4193: 4188: 4184: 4180: 4179:PLOS Genetics 4176: 4169: 4161: 4157: 4152: 4147: 4143: 4139: 4135: 4131: 4127: 4120: 4112: 4108: 4103: 4098: 4093: 4088: 4084: 4080: 4076: 4069: 4061: 4057: 4052: 4047: 4043: 4039: 4035: 4031: 4027: 4020: 4012: 4008: 4003: 3998: 3994: 3990: 3986: 3982: 3978: 3974: 3970: 3962: 3954: 3950: 3945: 3940: 3936: 3932: 3928: 3924: 3920: 3913: 3905: 3901: 3896: 3891: 3886: 3881: 3877: 3873: 3869: 3862: 3860: 3851: 3847: 3842: 3837: 3833: 3829: 3825: 3821: 3817: 3810: 3802: 3798: 3793: 3788: 3784: 3780: 3776: 3772: 3768: 3761: 3753: 3749: 3745: 3741: 3737: 3733: 3729: 3725: 3721: 3717: 3709: 3701: 3697: 3692: 3687: 3683: 3679: 3675: 3671: 3667: 3660: 3652: 3648: 3643: 3638: 3633: 3628: 3624: 3620: 3616: 3609: 3601: 3597: 3592: 3587: 3583: 3579: 3575: 3571: 3567: 3560: 3552: 3548: 3543: 3538: 3534: 3530: 3526: 3522: 3518: 3511: 3503: 3499: 3494: 3489: 3484: 3479: 3475: 3471: 3467: 3460: 3452: 3448: 3443: 3438: 3434: 3430: 3426: 3422: 3418: 3411: 3403: 3399: 3394: 3389: 3385: 3381: 3377: 3373: 3369: 3362: 3354: 3350: 3345: 3340: 3336: 3332: 3328: 3324: 3320: 3313: 3305: 3301: 3296: 3291: 3286: 3281: 3277: 3273: 3269: 3262: 3254: 3250: 3245: 3240: 3235: 3230: 3227:(1): lqz024. 3226: 3222: 3218: 3211: 3203: 3199: 3194: 3189: 3186:(5): 110443. 3185: 3181: 3177: 3170: 3162: 3158: 3153: 3148: 3143: 3138: 3134: 3130: 3126: 3119: 3111: 3107: 3102: 3097: 3093: 3089: 3085: 3081: 3077: 3073: 3069: 3062: 3054: 3050: 3046: 3042: 3038: 3034: 3030: 3026: 3019: 3011: 3007: 3003: 2999: 2995: 2991: 2987: 2983: 2979: 2975: 2971: 2963: 2955: 2951: 2946: 2941: 2937: 2933: 2929: 2925: 2921: 2914: 2906: 2902: 2897: 2892: 2888: 2884: 2880: 2876: 2872: 2868: 2864: 2857: 2849: 2845: 2840: 2835: 2830: 2825: 2821: 2817: 2813: 2806: 2798: 2794: 2789: 2784: 2779: 2774: 2770: 2766: 2762: 2755: 2747: 2743: 2739: 2735: 2731: 2727: 2723: 2719: 2711: 2703: 2699: 2694: 2689: 2685: 2681: 2677: 2673: 2669: 2665: 2661: 2654: 2646: 2642: 2637: 2632: 2628: 2624: 2620: 2616: 2612: 2608: 2604: 2597: 2589: 2585: 2580: 2575: 2571: 2567: 2563: 2559: 2555: 2548: 2540: 2536: 2531: 2526: 2522: 2518: 2514: 2510: 2506: 2499: 2497: 2488: 2484: 2479: 2474: 2470: 2466: 2462: 2458: 2454: 2450: 2446: 2438: 2430: 2426: 2421: 2416: 2412: 2408: 2404: 2400: 2396: 2388: 2386: 2384: 2375: 2371: 2367: 2363: 2359: 2355: 2351: 2347: 2343: 2339: 2332: 2330: 2321: 2317: 2313: 2309: 2305: 2301: 2297: 2293: 2289: 2285: 2277: 2269: 2265: 2261: 2257: 2253: 2249: 2245: 2241: 2237: 2233: 2226: 2224: 2222: 2220: 2211: 2207: 2202: 2197: 2193: 2189: 2185: 2181: 2177: 2170: 2162: 2158: 2154: 2150: 2146: 2142: 2138: 2134: 2130: 2126: 2122: 2115: 2107: 2103: 2098: 2093: 2089: 2085: 2081: 2077: 2073: 2066: 2064: 2056: 2052: 2048: 2043: 2038: 2034: 2030: 2029:BioTechniques 2026: 2019: 2011: 2007: 2002: 1997: 1992: 1987: 1983: 1979: 1975: 1968: 1966: 1961: 1952: 1949: 1947: 1944: 1942: 1941:Sphinx (gene) 1939: 1937: 1934: 1932: 1929: 1927: 1924: 1923: 1917: 1915: 1911: 1907: 1903: 1898: 1896: 1895:β-thalassemia 1892: 1888: 1883: 1879: 1873: 1871: 1867: 1863: 1862:polymorphisms 1859: 1858:transcriptome 1854: 1852: 1848: 1844: 1840: 1836: 1832: 1828: 1824: 1820: 1815: 1813: 1809: 1804: 1800: 1796: 1792: 1788: 1783: 1781: 1777: 1772: 1768: 1763: 1759: 1755: 1751: 1747: 1743: 1739: 1738:breast cancer 1735: 1731: 1727: 1723: 1719: 1715: 1711: 1706: 1704: 1700: 1696: 1692: 1688: 1684: 1680: 1675: 1673: 1669: 1665: 1661: 1651: 1649: 1645: 1641: 1637: 1632: 1629: 1625: 1621: 1617: 1613: 1603: 1601: 1597: 1593: 1589: 1580: 1578: 1574: 1570: 1569:X–chromosome. 1566: 1562: 1558: 1554: 1549: 1545: 1541: 1537: 1527: 1525: 1521: 1517: 1513: 1509: 1504: 1499: 1497: 1493: 1489: 1485: 1481: 1471: 1469: 1465: 1460: 1456: 1451: 1447: 1443: 1439: 1435: 1431: 1426: 1422: 1418: 1414: 1413: 1407: 1405: 1401: 1397: 1393: 1388: 1384: 1380: 1376: 1372: 1362: 1361:(see above). 1360: 1356: 1352: 1348: 1344: 1339: 1335: 1331: 1327: 1323: 1319: 1315: 1311: 1301: 1299: 1295: 1291: 1287: 1283: 1279: 1275: 1271: 1267: 1263: 1259: 1255: 1251: 1241: 1239: 1235: 1231: 1227: 1223: 1219: 1215: 1211: 1207: 1203: 1193: 1191: 1187: 1182: 1178: 1174: 1170: 1160: 1158: 1153: 1149: 1145: 1141: 1137: 1133: 1129: 1125: 1121: 1117: 1107: 1105: 1101: 1097: 1093: 1089: 1085: 1081: 1077: 1072: 1068: 1064: 1060: 1055: 1053: 1050:, Xlsirt and 1049: 1044: 1039: 1035: 1030: 1028: 1024: 1020: 1017: 1013: 1009: 1005: 1001: 997: 992: 990: 985: 981: 977: 973: 969: 965: 964:phosphorylate 961: 957: 953: 949: 945: 941: 937: 933: 929: 925: 915: 913: 909: 904: 902: 898: 894: 890: 886: 882: 878: 874: 869: 867: 862: 860: 859:tumorigenesis 856: 852: 848: 843: 839: 835: 831: 827: 823: 819: 815: 811: 807: 802: 800: 796: 792: 777: 775: 771: 767: 763: 759: 755: 751: 746: 737: 735: 731: 727: 723: 719: 714: 709: 707: 703: 699: 698:transcription 695: 690: 680: 679: 675: 671: 667: 663: 649: 646: 643: 641: 638: 635: 633: 632: 628: 625: 622: 619: 618: 615: 612: 609: 606: 603: 600: 598: 595: 592: 589: 588: 585: 582: 579: 576: 573: 571: 570: 566: 563: 560: 557: 556: 553: 550: 547: 544: 541: 539: 538: 534: 531: 528: 525: 524: 521: 518: 515: 512: 509: 507: 504: 502:Plant, animal 501: 498: 497: 494: 491: 488: 486: 485:Random forest 483: 480: 478: 477: 473: 471: 470: 466: 463: 460: 459: 456: 453: 450: 448: 445: 442: 440: 439: 435: 433: 432: 428: 425: 422: 421: 418: 415: 412: 410: 406: 402: 399: 397: 395: 394: 390: 388:Plant, animal 387: 384: 383: 380: 377: 374: 372: 369: 366: 364: 363: 359: 357: 356: 352: 349: 346: 345: 342: 339: 336: 334: 331: 328: 326: 325: 321: 319: 318: 314: 311: 308: 307: 304: 301: 298: 296: 293: 290: 288: 287: 283: 281: 280: 276: 273: 270: 269: 265: 262: 259: 256: 253: 250: 247: 244: 241: 240: 232: 231:transcripts. 230: 226: 222: 217: 214: 209: 205: 195: 193: 189: 188: 183: 179: 174: 171: 167: 163: 159: 155: 150: 148: 144: 140: 135: 132:transcripts ( 131: 127: 123: 119: 115: 111: 107: 103: 93: 91: 87: 82: 80: 76: 72: 68: 64: 60: 56: 52: 48: 44: 40: 32: 19: 9842: 9838: 9828: 9795: 9791: 9784: 9749: 9745: 9735: 9710: 9706: 9699: 9670: 9666: 9659: 9617:(4): e5027. 9614: 9610: 9600: 9573: 9569: 9529: 9525: 9515: 9488: 9484: 9474: 9431: 9427: 9417: 9390: 9386: 9376: 9349: 9345: 9332: 9305: 9301: 9291: 9246: 9242: 9232: 9199: 9195: 9188: 9155: 9151: 9145: 9112: 9108: 9102: 9069: 9065: 9059: 9027:(1): 15–29. 9024: 9020: 9010: 8985: 8981: 8937: 8933: 8923: 8890: 8886: 8880: 8845: 8841: 8831: 8794: 8791:Biomolecules 8790: 8780: 8743: 8739: 8729: 8692: 8688: 8678: 8641: 8637: 8627: 8584: 8580: 8534: 8530: 8496: 8492: 8486: 8445: 8441: 8435: 8400: 8396: 8386: 8361: 8357: 8313: 8309: 8299: 8264: 8260: 8250: 8209: 8205: 8199: 8166: 8162: 8117: 8113: 8103: 8078: 8074: 8067: 8032: 8028: 8018: 7983: 7979: 7969: 7926: 7922: 7866: 7862: 7855: 7820: 7816: 7806: 7771: 7768:Open Biology 7767: 7757: 7724: 7720: 7714: 7698: 7667: 7663: 7653: 7639:{{ 7631:{{ 7624: 7622:, 7568: 7564: 7520: 7516: 7462: 7458: 7447: 7402: 7398: 7388: 7343: 7339: 7329: 7286: 7282: 7235: 7231: 7225: 7182: 7178: 7122: 7118: 7108: 7073: 7069: 7059: 7016: 7012: 7005: 6970: 6966: 6956: 6921: 6917: 6907: 6872: 6868: 6858: 6813: 6809: 6799: 6764: 6760: 6747: 6720: 6716: 6706: 6671: 6667: 6619: 6615: 6605: 6578: 6574: 6564: 6529: 6525: 6483: 6479: 6440:(2): 93–96. 6437: 6433: 6427: 6386: 6382: 6376: 6341: 6337: 6327: 6294: 6290: 6284: 6249: 6245: 6235: 6200: 6196: 6190: 6163: 6159: 6149: 6122: 6118: 6062: 6058: 6048: 6015: 6011: 5969: 5965: 5921: 5917: 5907: 5872: 5868: 5858: 5813: 5809: 5799: 5772: 5768: 5758: 5723: 5719: 5709: 5676: 5672: 5628: 5624: 5614: 5581: 5577: 5571: 5534: 5531:BMC Genomics 5530: 5520: 5485: 5482:Cell Reports 5481: 5471: 5436: 5432: 5422: 5379: 5375: 5365: 5322: 5318: 5308: 5281: 5277: 5239:(1): 55–60. 5236: 5232: 5225: 5190: 5186: 5176: 5135: 5131: 5120: 5095: 5091: 5081: 5046: 5042: 4996: 4992: 4948: 4945:Cell Reports 4944: 4934: 4891: 4887: 4839: 4835: 4825: 4790: 4786: 4776: 4739: 4735: 4725: 4698: 4694: 4684: 4651: 4647: 4641: 4609:(1): 45–48. 4606: 4602: 4592: 4557: 4553: 4543: 4508: 4505:Cell Reports 4504: 4494: 4461: 4457: 4451: 4414: 4410: 4400: 4365: 4361: 4351: 4314: 4310: 4264: 4260: 4254: 4229: 4225: 4219: 4182: 4178: 4168: 4133: 4129: 4119: 4082: 4078: 4068: 4033: 4029: 4019: 3976: 3972: 3961: 3926: 3922: 3912: 3875: 3871: 3823: 3819: 3809: 3774: 3770: 3760: 3719: 3715: 3708: 3673: 3669: 3659: 3622: 3618: 3608: 3573: 3569: 3559: 3524: 3520: 3510: 3473: 3469: 3459: 3427:(17): e166. 3424: 3420: 3410: 3375: 3371: 3361: 3326: 3322: 3312: 3295:10754/631240 3275: 3271: 3261: 3224: 3220: 3210: 3183: 3179: 3169: 3132: 3129:BMC Genomics 3128: 3118: 3075: 3071: 3061: 3028: 3024: 3018: 2977: 2973: 2962: 2927: 2923: 2913: 2870: 2866: 2856: 2819: 2815: 2805: 2768: 2764: 2754: 2721: 2717: 2710: 2667: 2663: 2653: 2610: 2606: 2596: 2564:(1): 11–19. 2561: 2557: 2547: 2512: 2508: 2452: 2448: 2437: 2402: 2398: 2341: 2337: 2287: 2283: 2276: 2235: 2231: 2183: 2179: 2169: 2128: 2124: 2114: 2079: 2075: 2054: 2032: 2028: 2018: 1981: 1977: 1899: 1874: 1855: 1845:affected by 1816: 1784: 1730:malignancies 1707: 1676: 1657: 1633: 1616:genetic loci 1609: 1586: 1533: 1500: 1477: 1455:genomic loci 1410: 1408: 1368: 1307: 1247: 1199: 1166: 1136:housekeeping 1113: 1071:cancer cells 1056: 1031: 1004:Alu elements 993: 921: 905: 870: 863: 855:colon cancer 826:neurogenesis 803: 788: 768:regulation, 747: 743: 726:splice sites 710: 686: 683:Conservation 659: 629: 607:codon model 605:Phylogenetic 567: 535: 474: 467: 436: 429: 391: 360: 353: 322: 315: 284: 279:PLEKv2 Paper 277: 260:Training set 218: 201: 185: 175: 166:cell subtype 151: 134:tiling array 112:, including 99: 83: 46: 42: 38: 37: 9667:Circulation 5278:Cancer Cell 5092:Development 4742:: 153–172. 2076:RNA Biology 1906:vaccination 1812:development 1710:tumor cells 1695:cytoplasmic 1664:multi-omics 1383:sumoylation 1347:pseudogenes 1334:transcripts 1250:translation 1234:mesenchymal 1226:splice site 1196:In splicing 912:chromosomal 702:orthologous 656:Translation 574:FASTA, GTF 407:length and 251:Repository 248:Web server 59:nucleotides 55:transcripts 43:long ncRNAs 9892:Categories 8797:(4): 550. 4085:(5): R49. 3878:: e08890. 3625:(19): 19. 3527:(8): e57. 3476:(1): 311. 3329:(6): e74. 3135:(1): 756. 1957:References 1843:cell types 1758:metastasis 1699:Alu repeat 1600:telomerase 1538:in female 1488:chromosome 1484:imprinting 1474:Imprinting 1412:Drosophila 1324:and mouse 1322:Drosophila 1256:where the 1159:in trans. 1076:heat shock 1059:heat shock 1027:heat shock 952:chromosome 901:epigenetic 791:eukaryotes 694:vertebrate 674:translated 636:FASTA, BED 510:FASTA, GTF 409:GC content 266:Reference 254:Input file 204:intergenic 114:5' capping 77:(piRNAs), 73:(siRNAs), 69:(miRNAs), 65:, such as 9224:260632006 9115:: 13–22. 8478:205001095 8035:: 55–66. 7706:CC BY 4.0 7641:retracted 7633:retracted 7021:CiteSeerX 6205:CiteSeerX 6197:BioEssays 5339:2001-0370 4908:1362-4962 3752:205253245 3378:(1): e2. 2887:1362-4962 2822:(2): 36. 2684:1362-4962 2613:: 32753. 2161:258528357 2145:1471-0080 2031:(paper). 1984:(1): 17. 1951:ZNRD1-AS1 1887:antisense 1851:haplotype 1780:epidermis 1776:psoriasis 1588:Telomeres 1579:mammals. 1480:chromatin 1425:Hox genes 1396:stem cell 1387:chromatin 1330:annealing 1258:dendritic 1222:antisense 1173:microRNAs 936:promoters 914:domains. 885:cyclin D1 851:apoptosis 847:leukaemia 822:forebrain 740:Functions 713:conserved 590:PhyloCSF 443:FASTA/BED 347:RNAsamba 309:DeepPlnc 187:in-silico 170:neocortex 96:Abundance 67:microRNAs 9879:31399544 9812:12730694 9776:18587408 9727:15294872 9691:38557125 9651:19343170 9611:PLOS ONE 9592:19592466 9548:18048406 9507:17440112 9466:17478681 9409:17066261 9368:15855153 9283:15738415 9216:15221013 9196:Oncogene 9172:16878148 9152:Oncogene 9137:53569324 9129:30445017 9094:26576988 9086:25035150 9051:34727260 9002:16569192 8915:39305428 8872:30329098 8823:33918762 8772:32144193 8721:25569254 8670:23593023 8619:20693275 8611:17916692 8551:18157120 8513:17876321 8427:14749728 8378:17869504 8340:12456662 8291:11562346 8234:11845212 8191:19084498 8183:15516932 8144:16702402 8095:10369866 8059:16117633 8010:17445943 7961:18185590 7899:34559885 7891:16141073 7798:32898472 7749:16059065 7741:17690303 7708:license. 7694:32055844 7620:24876484 7601:16423723 7593:16497925 7547:17604720 7509:Chang HY 7481:18555785 7439:18000552 7399:PLOS ONE 7321:17603471 7260:23292265 7252:17304537 7217:18535243 7157:18463631 7100:18691963 7051:18840384 7043:15302134 6997:17699670 6948:16330711 6753:Tiedge H 6698:18347095 6646:23178169 6597:17264081 6556:17977614 6508:41151259 6500:17018852 6462:10513502 6454:15593371 6368:16781978 6360:12676327 6319:28643222 6311:11780141 6276:18299392 6227:14505360 6182:18313380 6141:18313387 6089:17307818 6040:22199826 6032:15300239 5994:11997028 5986:15565108 5899:12466850 5850:11237011 5791:14580347 5750:11604515 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