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Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates.

Wen J, Ladewig E, Shenker S, Mohammed J, Lai EC - PLoS Comput. Biol. (2015)

Bottom Line: While mirtrons generate miRNA-class regulatory RNAs, we also find that mirtrons exhibit many features that distinguish them from canonical miRNAs.We observe that conventional mirtron hairpins are substantially longer than Drosha-generated pre-miRNAs, indicating that the characteristic length of canonical pre-miRNAs is not a general feature of Dicer substrate hairpins.In addition, mammalian mirtrons exhibit unique patterns of ordered 5' and 3' heterogeneity, which reveal hidden complexity in miRNA processing pathways.

View Article: PubMed Central - PubMed

Affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, United States of America.

ABSTRACT
Mirtrons are microRNA (miRNA) substrates that utilize the splicing machinery to bypass the necessity of Drosha cleavage for their biogenesis. Expanding our recent efforts for mammalian mirtron annotation, we use meta-analysis of aggregate datasets to identify ~500 novel mouse and human introns that confidently generate diced small RNA duplexes. These comprise nearly 1000 total loci distributed in four splicing-mediated biogenesis subclasses, with 5'-tailed mirtrons as, by far, the dominant subtype. Thus, mirtrons surprisingly comprise a substantial fraction of endogenous Dicer substrates in mammalian genomes. Although mirtron-derived small RNAs exhibit overall expression correlation with their host mRNAs, we observe a subset with substantial differences that suggest regulated processing or accumulation. We identify characteristic sequence, length, and structural features of mirtron loci that distinguish them from bulk introns, and find that mirtrons preferentially emerge from genes with larger numbers of introns. While mirtrons generate miRNA-class regulatory RNAs, we also find that mirtrons exhibit many features that distinguish them from canonical miRNAs. We observe that conventional mirtron hairpins are substantially longer than Drosha-generated pre-miRNAs, indicating that the characteristic length of canonical pre-miRNAs is not a general feature of Dicer substrate hairpins. In addition, mammalian mirtrons exhibit unique patterns of ordered 5' and 3' heterogeneity, which reveal hidden complexity in miRNA processing pathways. These include broad 3'-uridylation of mirtron hairpins, atypically heterogeneous 5' termini that may result from exonucleolytic processing, and occasionally robust decapitation of the 5' guanine (G) of mirtron-5p species defined by splicing. Altogether, this study reveals that this extensive class of non-canonical miRNA bears a multitude of characteristic properties, many of which raise general mechanistic questions regarding the processing of endogenous hairpin transcripts.

No MeSH data available.


Related in: MedlinePlus

Distinct patterns of terminal heterogeneity in mirtron-derived small RNAs.(A, B) 5'-end heterogeneity in the 5p and 3p reads from human (A) and mouse (B) miRNA loci. There are several distinctions between canonical miRNAs and specific classes of mirtrons. These include substantial populations of mirtron-5p reads that lack their 5' nucleotide defined by splice donor sites, namely 5p reads from conventional mirtrons and 3' tailed mirtrons (*), and overall greater 5' heterogeneity in the 5' reads from 5' tailed mirtrons (#). (C, D) 3'-end heterogeneity in the 5p and 3p reads from human (C) and mouse (D) miRNA loci. Particularly notable are the dominant populations of 3'-tailed reads from 3p arms of conventional mirtrons and 5'-tailed mirtrons (marked by + signs), i.e., those reads that are defined by splice acceptor sites.
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pcbi.1004441.g006: Distinct patterns of terminal heterogeneity in mirtron-derived small RNAs.(A, B) 5'-end heterogeneity in the 5p and 3p reads from human (A) and mouse (B) miRNA loci. There are several distinctions between canonical miRNAs and specific classes of mirtrons. These include substantial populations of mirtron-5p reads that lack their 5' nucleotide defined by splice donor sites, namely 5p reads from conventional mirtrons and 3' tailed mirtrons (*), and overall greater 5' heterogeneity in the 5' reads from 5' tailed mirtrons (#). (C, D) 3'-end heterogeneity in the 5p and 3p reads from human (C) and mouse (D) miRNA loci. Particularly notable are the dominant populations of 3'-tailed reads from 3p arms of conventional mirtrons and 5'-tailed mirtrons (marked by + signs), i.e., those reads that are defined by splice acceptor sites.

Mentions: We analyzed terminal heterogeneities at the 5' ends and 3' ends of 5p-arm and 3p-arm reads from the three classes of mirtrons, and compared these to canonical miRNAs (Fig 6). We indeed observed that specific mirtron classes exhibit substantially increased terminal heterogeneity. For example, we observe that the 5' ends of 5p-arm reads of 3'-tailed mirtrons exhibited relatively diffuse start positions upstream and downstream of the dominant 5' end (Fig 6A and 6B, poundsigns), whereas conventional and 5' tailed mirtrons exhibited directional heterogeneity 1-nt downstream of the dominant 5' start of 5p-arm reads defined by the splice donor reference, particularly in human data (Fig 6A, asterisks). On the other hairpin side, we observed clear signatures in which the 3' termini of 3p-arm reads from conventional and 5'-tailed mirtrons were dominantly extended by one nucleotide from the splice acceptor reference (Fig 6C and 6D, plus-signs).


Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates.

Wen J, Ladewig E, Shenker S, Mohammed J, Lai EC - PLoS Comput. Biol. (2015)

Distinct patterns of terminal heterogeneity in mirtron-derived small RNAs.(A, B) 5'-end heterogeneity in the 5p and 3p reads from human (A) and mouse (B) miRNA loci. There are several distinctions between canonical miRNAs and specific classes of mirtrons. These include substantial populations of mirtron-5p reads that lack their 5' nucleotide defined by splice donor sites, namely 5p reads from conventional mirtrons and 3' tailed mirtrons (*), and overall greater 5' heterogeneity in the 5' reads from 5' tailed mirtrons (#). (C, D) 3'-end heterogeneity in the 5p and 3p reads from human (C) and mouse (D) miRNA loci. Particularly notable are the dominant populations of 3'-tailed reads from 3p arms of conventional mirtrons and 5'-tailed mirtrons (marked by + signs), i.e., those reads that are defined by splice acceptor sites.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4556696&req=5

pcbi.1004441.g006: Distinct patterns of terminal heterogeneity in mirtron-derived small RNAs.(A, B) 5'-end heterogeneity in the 5p and 3p reads from human (A) and mouse (B) miRNA loci. There are several distinctions between canonical miRNAs and specific classes of mirtrons. These include substantial populations of mirtron-5p reads that lack their 5' nucleotide defined by splice donor sites, namely 5p reads from conventional mirtrons and 3' tailed mirtrons (*), and overall greater 5' heterogeneity in the 5' reads from 5' tailed mirtrons (#). (C, D) 3'-end heterogeneity in the 5p and 3p reads from human (C) and mouse (D) miRNA loci. Particularly notable are the dominant populations of 3'-tailed reads from 3p arms of conventional mirtrons and 5'-tailed mirtrons (marked by + signs), i.e., those reads that are defined by splice acceptor sites.
Mentions: We analyzed terminal heterogeneities at the 5' ends and 3' ends of 5p-arm and 3p-arm reads from the three classes of mirtrons, and compared these to canonical miRNAs (Fig 6). We indeed observed that specific mirtron classes exhibit substantially increased terminal heterogeneity. For example, we observe that the 5' ends of 5p-arm reads of 3'-tailed mirtrons exhibited relatively diffuse start positions upstream and downstream of the dominant 5' end (Fig 6A and 6B, poundsigns), whereas conventional and 5' tailed mirtrons exhibited directional heterogeneity 1-nt downstream of the dominant 5' start of 5p-arm reads defined by the splice donor reference, particularly in human data (Fig 6A, asterisks). On the other hairpin side, we observed clear signatures in which the 3' termini of 3p-arm reads from conventional and 5'-tailed mirtrons were dominantly extended by one nucleotide from the splice acceptor reference (Fig 6C and 6D, plus-signs).

Bottom Line: While mirtrons generate miRNA-class regulatory RNAs, we also find that mirtrons exhibit many features that distinguish them from canonical miRNAs.We observe that conventional mirtron hairpins are substantially longer than Drosha-generated pre-miRNAs, indicating that the characteristic length of canonical pre-miRNAs is not a general feature of Dicer substrate hairpins.In addition, mammalian mirtrons exhibit unique patterns of ordered 5' and 3' heterogeneity, which reveal hidden complexity in miRNA processing pathways.

View Article: PubMed Central - PubMed

Affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York, United States of America.

ABSTRACT
Mirtrons are microRNA (miRNA) substrates that utilize the splicing machinery to bypass the necessity of Drosha cleavage for their biogenesis. Expanding our recent efforts for mammalian mirtron annotation, we use meta-analysis of aggregate datasets to identify ~500 novel mouse and human introns that confidently generate diced small RNA duplexes. These comprise nearly 1000 total loci distributed in four splicing-mediated biogenesis subclasses, with 5'-tailed mirtrons as, by far, the dominant subtype. Thus, mirtrons surprisingly comprise a substantial fraction of endogenous Dicer substrates in mammalian genomes. Although mirtron-derived small RNAs exhibit overall expression correlation with their host mRNAs, we observe a subset with substantial differences that suggest regulated processing or accumulation. We identify characteristic sequence, length, and structural features of mirtron loci that distinguish them from bulk introns, and find that mirtrons preferentially emerge from genes with larger numbers of introns. While mirtrons generate miRNA-class regulatory RNAs, we also find that mirtrons exhibit many features that distinguish them from canonical miRNAs. We observe that conventional mirtron hairpins are substantially longer than Drosha-generated pre-miRNAs, indicating that the characteristic length of canonical pre-miRNAs is not a general feature of Dicer substrate hairpins. In addition, mammalian mirtrons exhibit unique patterns of ordered 5' and 3' heterogeneity, which reveal hidden complexity in miRNA processing pathways. These include broad 3'-uridylation of mirtron hairpins, atypically heterogeneous 5' termini that may result from exonucleolytic processing, and occasionally robust decapitation of the 5' guanine (G) of mirtron-5p species defined by splicing. Altogether, this study reveals that this extensive class of non-canonical miRNA bears a multitude of characteristic properties, many of which raise general mechanistic questions regarding the processing of endogenous hairpin transcripts.

No MeSH data available.


Related in: MedlinePlus