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WIREs Syst Biol Med
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Noncoding RNAs in gene regulation

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Abstract RNAs have been traditionally viewed as intermediates between DNA and proteins. However, there is a growing body of literature indicating that noncoding RNAs (ncRNAs) are key players for gene regulation, genome stability, and chromatin modification. In addition to the well‐known small interfering RNAs and microRNAs acting in transcriptional and posttranscriptional gene silencing, recent advances in the field of transcriptome exploration have revealed novel sets of new small and large ncRNAs. Many of them appear to be conserved across mammals, and abnormal expression of several ncRNAs has been linked to a wide variety of human diseases, such as cancer. Here, we review the different classes of ncRNAs identified to date, in yeast and mammals, and we discuss the mechanisms by which they affect gene regulation. WIREs Syst Biol Med 2011 3 728–738 DOI: 10.1002/wsbm.148 This article is categorized under: Biological Mechanisms > Regulatory Biology

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Schematic representation of new classes of ncRNAs identified in eukaryotes. (a) Long ncRNAs in S. cerevisiae. Black, dark blue, and red arrows represent transcription start sites of mRNA, cryptic unstable transcripts (CUTs), and stable unannotated transcripts (SUTs), respectively. Gray boxes define protein‐coding genes. CUTs are produced by RNAPII, capped, polyadenylated by the TRAMP4 complex and degraded by the nuclear exosome. SUTs are produced by RNAPII, capped and polyadenylated. Whether SUTs are exported to the cytoplasm remains to be demonstrated. (b) Small and long mammalian ncRNAs. Arrows represent transcription start sites, with the following color code: black for mRNA, dark blue for PROMoter uPstream Transcripts (PROMPTs), red for large intergenic ncRNAs (lincRNAs), light gray for promoter‐associated long ncRNAs (PALRs), dark gray for terminator‐associated small RNAs (TASRs) and light blue for a group of short transcripts associated with mRNA transcription start sites, including promoter‐associated small RNAs (PASRs), transcription initiation RNAs (tiRNAs), and transcription start site‐associated RNAs (TSSa‐RNAs). The gray boxes define protein‐coding genes. Not represented in this figure: siRNAs, miRNAs, and piRNAs.

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Models for long ncRNA‐dependent regulation of gene expression in mammals. (a) Regulation in cis. The nascent antisense ANRIL transcript is bound by the Polycomb repressive complex 2 (PRC2) and PRC1 complexes and retains them at the transcription site, leading to PRC2‐mediated H3K27 trimethylation, PRC1 recruitment on the chromatin through its chromobox Protein 7 (CBX7) subunit and subsequent transcriptional repression of the INK4b/ARF/Ink4a locus. (b) Regulation in trans through recruitment of chromatin modification machineries. HOTAIR is produced from the HOXC locus and directs gene silencing at the HOXD locus by recruiting the PRC2 and CoREST/REST histone modification complexes, responsible for H3K27 trimethylation and H3K4 demethylation, respectively. (c) Regulation in trans through interaction with DNA‐binding factors. The lincRNA‐p21 is produced upon p53 induction, it interacts with the heterogeneous nuclear ribonucleoprotein K (hnRNP‐K), and this interaction leads to the specific transcriptional repression of prosurvival genes. HOX, Homeobox gene.

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Models for long ncRNA‐dependent regulation of gene expression in S. cerevisiae. (a) Regulation in cis: in the absence of the Rrp6 component of the nuclear exosome, a cryptic ncRNA (represented in dark blue) antisense to the PHO84 gene is stabilized and recruits the Hda1 HDAC complex, leading to histone deacetylation and PHO84 transcriptional silencing. (b) Regulation in trans: stabilization of a cryptic ncRNA, which is sensitive to the Xrn1‐dependent cytoplasmic 5′ → 3′ degradation pathway, leads to transcriptional silencing of the Ty1 retrotransposon through an unknown mechanism that involves the Set1 HMT and the associated H3K4 methylations. This ncRNA has also been implicated in Ty1 posttranscriptional silencing through translation inhibition.

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