Mammalian microRNAs derived from genomic repeats

Smalheiser, Neil R.; Torvik, Vetle I.

doi:10.1016/j.tig.2005.04.008

Cited by 268 publications

(214 citation statements)

References 18 publications

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“…Many of the least-conserved ES cell miRNA hairpins overlap annotated repetitive elements, suggesting that particular miRNAs may partially function to silence complementary repeat-containing RNAs (34,35). This repression could occur through a canonical miRNA-based targeting mechanism, resulting in the translational inhibition and targeting to cellular processing bodies of repeat-containing RNAs with seed complements to repeat-derived miRNAs.…”

Section: Discussionmentioning

confidence: 99%

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells

Calabrese

Seila

Yeo

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

301

269

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Short RNA expression was analyzed from Dicer -positive and Dicer -knockout mouse embroyonic stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can be accounted for by six distinct miRNA loci. Four of these miRNA loci or their human homologues have demonstrated roles in cell cycle regulation or oncogenesis, suggesting that a major function of the miRNA pathway in ES cells may be to shape their distinct cell cycle. Forty-six previously uncharacterized miRNAs were identified, most of which are expressed at low levels and are less conserved than the set of known miRNAs. Low-abundance short RNAs matching all classes of repetitive elements were present in cells lacking Dicer , although the production of some SINE- and simple repeat-associated short RNAs appeared to be Dicer-dependent. These and other Dicer-dependent sequences resembled miRNAs. At a depth of sequencing that approaches the total number of 5′ phosphorylated short RNAs per cell, miRNAs appeared to be Dicer's only substrate. The results presented suggest a model in which repeat-associated miRNAs serve as host defenses against repetitive elements, a function canonically ascribed to other classes of short RNA.

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Section: Discussionmentioning

confidence: 99%

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells

Calabrese

Seila

Yeo

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

301

269

View full text Add to dashboard Cite

show abstract

“…In addition, the regulation of gene expression by miRNAs may be a relatively easy innovation, particularly when triggering transcript cleavage as in plants. As recently proposed (Allen et al 2004;Smalheiser and Torvik 2005), at least some miRNA genes may arise from inverted duplications of target gene sequences and the initially produced double stranded foldback transcripts may operate as regulators via the degradative RNAi pathway. Progressive sequence degradation, under selective pressure, may eventually result in the bulged structure typical of miRNA precursors.…”

Section: Summary and Perspectivementioning

confidence: 94%

On the origin and functions of RNA-mediated silencing: from protists to man

2006

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Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways. We have examined the taxonomic distribution and the phylogenetic relationship of key components of the RNA interference (RNAi) machinery in members of five eukaryotic supergroups. On the basis of the parsimony principle, our analyses suggest that a relatively complex RNAi machinery was already present in the last common ancestor of eukaryotes and consisted, at a minimum, of one Argonautelike polypeptide, one Piwi-like protein, one Dicer, and one RNAdependent RNA polymerase. As proposed before, the ancestral (but non-essential) role of these components may have been in defense responses against genomic parasites such as transposable elements and viruses. From a mechanistic perspective, the RNAi machinery in the eukaryotic ancestor may have been capable of both small-RNA-guided transcript degradation as well as transcriptional repression, most likely through histone modifications. Both roles appear to be widespread among living eukaryotes and this diversification of function could account for the evolutionary conservation of duplicated Argonaute-Piwi proteins. In contrast, additional RNAi-mediated pathways such as RNA-directed DNA methylation, programmed genome rearrangements, meiotic silencing by unpaired DNA, and miRNA-mediated gene regulation may have evolved independently in specific lineages.

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“…A lot of regulatory small RNAs including mi RNAs have been shown to have the origin in repetitive elements [27,28]. Several non-coding RNAs like snoRNAs, tRNAs, rRNAs and other non-coding RNAs have been reported to produce endogenous regulatory small RNAs capable to influence phenotypes in vertebrates [29][30][31]. Besides this, endogenous regulatory small RNAs are now also reported from corners which were earlier blindly filtered out from genomic studies as a practice [32,33].…”

Section: Rna Biogenesismentioning

confidence: 99%

“…Several non-coding RNAs like snoRNAs, tRNAs, rRNAs and other non-coding RNAs have been reported to produce endogenous regulatory small RNAs capable to influence phenotypes in vertebrates [29][30][31]. Besides this, endogenous regulatory small RNAs are now also reported from corners which were earlier blindly filtered out from genomic studies as a practice [32,33]. Several non-coding RNAs like snoRNAs, tRNAs, rRNAs and other non-coding RNAs have been reported to produce endogenous regulatory small RNAs capable to influence phenotypes in vertebrates [33][34][35].…”

Section: Rna Biogenesismentioning

confidence: 99%

Peculiarities of Non Coding Micrornas Organization in H. Sapiens and some other Species

Ns¹

2017

IJMBOA

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It is universally accepted today that micro (mi) non coding (nc) RNAs are endogenous ~22 nt RNAs that can play important regulatory roles in a vast number of cellular processes including cell growth, disease, embryogenesis, gene regulation, signal transduction, receptor activation, etc. by targeting mRNAs for cleavage or translational repression. Mi RNAs comprise one of the more abundant classes of gene regulatory molecules in multi cellular organisms and likely influence the output of many protein-coding genes. The shorter lin-4 RNA is now recognized as the founding member of an abundant class of tiny regulatory RNAs called micro RNAs or mi RNAs. Now it has become clear that large number of regulatory small (rs) RNAs are compromised due to traditional approaches to identify mi RNAs mainly to hair-pin loop bred typical signs. The rsRNA-target interactions have been studied with the use of mi RNA recognition elements binding with Ago proteins (AGO-cross linking), microprocessor complex subunit DGCR8 involved in the initial step of mi RNA biogenesis cross-linking, ligation, and sequencing of hybrids (CLASH), proteome and expression data. The advent of next generation sequencing (NGS) technologies, powerful enough to detect most of the existing small (s) RNA sequences even with low abundance, gave rise to a sudden surge in the reporting of novel mi RNAs.

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Mammalian microRNAs derived from genomic repeats

Cited by 268 publications

References 18 publications

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells

On the origin and functions of RNA-mediated silencing: from protists to man

Peculiarities of Non Coding Micrornas Organization in H. Sapiens and some other Species

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