Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci

Tyler, David M.; Okamura, Katsutomo; Chung, Wei Jen; Hagen, Joshua W.; Berezikov, Eugène; Hannon, Gregory J.; Lai, Eric C.

doi:10.1101/gad.1615208

Cited by 183 publications

(226 citation statements)

References 32 publications

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“…These findings suggest that with the continuous availability of genome sequences, we could identify many more miRNAs that regulate important genes in B. rapa. The transcription of miRNAs from sense and antisense strands is recently reported in insects, human, and plants (Bender, 2008;Stark et al, 2008;Tyler et al, 2008;Zhang et al, 2008). In the present study, we found only 1 DNA sequence from which both sense and antisense mature miRNAs were produced compared to 5 miRNAs belonging to 3 families identified in soybean ; the sense and antisense miRNAs differ by 1-3 nt in that study.…”

Section: Discussionsupporting

confidence: 51%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20 th position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

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Section: Discussionsupporting

confidence: 51%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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“…It has been described previously that miRNA loci can be transcribed from both strands to form mature miRNAs (Ruby et al 2007a;Tyler et al 2008). We found one locus that produced putative miRNAs from both directions and one locus that only produced an antisense miRNA to a known miRNA.…”

Section: Discussionmentioning

confidence: 66%

Repertoire and evolution of miRNA genes in four divergent nematode species

Wit

Linsen²,

Cuppen³

et al. 2009

Genome Res.

Self Cite

112

133

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miRNAs are ∼22-nt RNA molecules that play important roles in post-transcriptional regulation. We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei, and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. Interestingly, more than half of all identified miRNA genes are conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed “hairpin shifting,” in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation.

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“…As more highthroughput data is acquired, these as well as other antisense loci are likely to be annotated as miRNA genes. However, <0.00002 of our miRNA reads corresponded to miRNAs from antisense loci (excluding the reads mapping ambiguously to mir-486/mir-3107), raising the possibility that none of the murine antisense miRNAs have a function comparable with that of miR-iab-as in flies (Bender 2008;Stark et al 2008;Tyler et al 2008).…”

Section: General Features Of Mammalian Mirnasmentioning

confidence: 97%

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

Chiang

Schoenfeld²,

Ruby³

et al. 2010

Genes Dev.

750

756

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MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60 million small RNAs from mouse brain, ovary, testes, embryonic stem cells, three embryonic stages, and whole newborns. Analysis of these sequences confirmed 398 annotated miRNA genes and identified 108 novel miRNA genes. More than 150 previously annotated miRNAs and hundreds of candidates failed to yield sequenced RNAs with miRNA-like features. Ectopically expressing these previously proposed miRNA hairpins also did not yield small RNAs, whereas ectopically expressing the confirmed and newly identified hairpins usually did yield small RNAs with the classical miRNA features, including dependence on the Drosha endonuclease for processing. These experiments, which suggest that previous estimates of conserved mammalian miRNAs were inflated, provide a substantially revised list of confidently identified murine miRNAs from which to infer the general features of mammalian miRNAs. Our analyses also revealed new aspects of miRNA biogenesis and modification, including tissue-specific strand preferences, sequential Dicer cleavage of a metazoan precursor miRNA (pre-miRNA), consequential 59 heterogeneity, newly identified instances of miRNA editing, and evidence for widespread pre-miRNA uridylation reminiscent of miRNA regulation by Lin28.[Keywords: MicroRNA; miRNA biogenesis; noncoding RNA genes; high-throughput sequencing] Supplemental material is available at http://www.genesdev.org.

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Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci

Cited by 183 publications

References 32 publications

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Repertoire and evolution of miRNA genes in four divergent nematode species

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

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