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Lives that introns lead after splicing

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After transcription of a eukaryotic pre‐mRNA, its introns are removed by the spliceosome, joining exons for translation. The intron products of splicing have long been considered ‘junk’ and destined only for destruction. But because they are large in size and under weak selection constraints, many introns have been evolutionarily repurposed to serve roles after splicing. Some spliced introns are precursors for further processing of other encoded RNAs such as small nucleolar RNAs, microRNAs, and long noncoding RNAs. Other intron products have long half‐lives and can be exported to the cytoplasm, suggesting that they have roles in translation. Some viruses encode introns that accumulate after splicing and play important but mysterious roles in viral latency. Turnover of most lariat‐introns is initiated by cleavage of their internal 2′‐5′ phosphodiester bonds by a unique debranching endonuclease, and the linear products are further degraded by exoribonucleases. However, several introns appear to evade this turnover pathway and the determinants of their stability are largely unknown. Whereas many stable intron products were discovered serendipitously, new experimental and computational tools will enable their direct identification and study. Finally, the origins and mechanisms of mobility of eukaryotic introns are mysterious, and mechanistic studies of the intron life cycle may yield new insights into how they arose and became widespread. WIREs RNA 2013, 4:677–691. doi: 10.1002/wrna.1187 This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms

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Classification of branched RNA. Summary of branched RNA classes and their biogenesis, turnover, and function.
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Putative mechanisms of intron transposition. (a) Following the first step of splicing, Prp22 mediates release of the messenger RNA (mRNA) product. Prior to release of the lariat‐intron, a new ‘proto’ pre‐mRNA is loaded into this spliceosome, and reversal of the second and first catalytic steps yields a new pre‐mRNA. (b) Following the first step of splicing, Prp43 mediates release of the lariat‐intron without releasing the mRNA product. A second lariat‐intron is loaded into this spliceosome, and reversal of the second and first catalytic steps yields a new pre‐mRNA. (c) The putative products of both (a) and (b) are reverse transcribed and recombined into their original genomic locus, representing intron acquisition and intron exchange events, respectively.
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Alternative fates of lariat‐intermediates and lariat‐introns after splicing. (a) After splicing, lariat‐intermediates can be exported to the cytoplasm and translated via an IRES, but it is not known whether endogenous lariat‐intermediates are translated. (b) Lariat‐introns can accumulate in the nucleus, where they have been associated with repressive chromatin complexes, and are restricted from export in Xenopus oocytes. Stable lariat‐introns might sequester free nucleotides for further rounds of transcription. Latency‐associated introns from some viruses are stable in cells, where they can promote viral latency and associate with ribosomes.
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Creation and destruction of branched RNA. (a) The first two steps of genic splicing yield a lariat‐intermediate and lariat‐intron, respectively. The lariat‐intermediate can be discarded by Prp43, and is subject to further turnover by Dbr1, or possibly an unidentified nuclease activity. Debranched lariat‐intermediates can subsequently be degraded by Xrn1 (a 5′‐3′ exonuclease) or Ski2 (a component of the cytoplasmic 3′‐5′ exoribonuclease). Lariat‐introns are disassembled from spliceosomal complexes by Prp43, and can be further processed by debranching, endonucleolytic cleavage by Rnt1, or additional nucleolytic pathways. Some lariat‐introns are precursors for small nucleolar RNA (snoRNA) or mirtrons processing. (b) In SL trans‐splicing, primary transcripts are transcribed and are spliced to the SL RNA, yielding a messenger RNA (mRNA) and a Y‐form branched product, which is presumably degraded by Dbr1. The sequence of the ‘outron’ portion of the Y‐form branched RNA represents the site of transcription initiation, and can be used to annotation transcription start sites.
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