Evolution, biogenesis and function of promoter-associated RNAs

Taft, Ryan J.; Kaplan, Craig D.; Simons, Cas; Mattick, John S.

doi:10.4161/cc.8.15.9154

Cited by 86 publications

(91 citation statements)

References 54 publications

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“…The discovery of numerous small noncoding RNA (sncRNA) species encoded by the nuclear genome, including microRNAs (miRNAs) [11][12][13], piwi-interacting RNAs (piRNAs) [14][15][16], endogenous small interfering RNAs (endo-siRNAs) [17][18][19][20] and promoter-associated small RNAs (PASRs) [21][22][23], has changed our view on the regulation of gene expression because we now know…”

Section: Introductionmentioning

confidence: 99%

The mitochondrial genome encodes abundant small noncoding RNAs

et al. 2013

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Small noncoding RNAs identified thus far are all encoded by the nuclear genome. Here, we report that the murine and human mitochondrial genomes encode thousands of small noncoding RNAs, which are predominantly derived from the sense transcripts of the mitochondrial genes (host genes), and we termed these small RNAs mitochondrial genome-encoded small RNAs (mitosRNAs). DICER inactivation affected, but did not completely abolish mitosRNA production. MitosRNAs appear to be products of currently unidentified mitochondrial ribonucleases. Overexpression of mitosRNAs enhanced expression levels of their host genes in vitro, and dysregulated mitosRNA expression was generally associated with aberrant mitochondrial gene expression in vivo. Our data demonstrate that in addition to 37 known mitochondrial genes, the mammalian mitochondrial genome also encodes abundant mitosRNAs, which may play an important regulatory role in the control of mitochondrial gene expression in the cell.

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Section: Introductionmentioning

confidence: 99%

The mitochondrial genome encodes abundant small noncoding RNAs

et al. 2013

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“…1,2 In addition, small RNAs have been found to be associated with transcription start and stop sites of mRNAs. [3][4][5] Several studies reported that well-known ncRNA loci are also processed to give rise to small RNAs. MicroRNA precursor hairpins, for instance, are frequently processed to produce additional "off-set RNAs" (moRNAs) that appear to function like mature miRs.…”

Section: Introductionmentioning

confidence: 99%

Identification and Classification of Small Rnas in Transcriptome Sequence Data

et al. 2009

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Current methods for high throughput sequencing (HTS) for the first time offer the opportunity to investigate the entire transcriptome in an essentially unbiased way. In many species, small non-coding RNAs with specific secondary structures constitute a significant part of the transcriptome. Some of these RNA classes, in particular microRNAs and snoRNAs, undergo maturation processes that lead to the production of shorter RNAs. After mapping the sequences to the reference genome specific patterns of short reads can be observed. These read patterns seem to reflect the processing and thus are specific for the RNA transcripts of which they are derived from. We explore here the potential of short read sequence data in the classification and identification of non-coding RNAs.

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“…Nucleosomal shifting as small as 30 bp at transcription start sites (TSS) has been implicated in radical changes in the activity of RNA polymerase II (RNAPII). 7 The first nucleosome downstream of the TSS may also act as a barrier that induces RNAPII pausing and backtracking to produce tiRNAs 8 and that enforces the positioning of following nucleosomes. The latter notion is supported by the finding that the average nucleosome occupancy downstream of active TSSs is phased and gradually dissipates as the distance from the TSS approaches 1 kb.…”

Section: Introductionmentioning

confidence: 99%