Mechanisms of Alternative Pre-Messenger RNA Splicing

Black, Douglas L.

doi:10.1146/annurev.biochem.72.121801.161720

Cited by 2,327 publications

(2,333 citation statements)

References 368 publications

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“…The rewriting of RNA restores the correct reading frame, allowing the production of functional gene products. RNA guides are also used to direct rewriting of RNA during editing and splicing of pre-mRNA 3,67 . In some cases, editing targets splice sites and in others, splicing prevents editing 67 .…”

Section: Rna-directed Rewriting Of Rnamentioning

confidence: 99%

The four Rs of RNA-directed evolution

Herbert

2003

Nat Genet

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The read-out of genetic information in eukaryotes is not only more complex than previously realized, but also more dynamic. Much of the information is 'soft-wired' , with extensive RNA processing necessary to generate phenotypes 10 . A subset of the RNA, referred to here as coRNA ( Fig. 1), coordinates the read-out of genetic information and reconciles regulatory inputs. For each cell type, the sum of these interactions defines a distinct RNA profile or ribotype 10 . RNA-based processes also facilitate replication of ribotypes in subsequent generations. The flexibility of these programs allows soft-wired organisms to evolve in a more rapid and dynamic way than 'hard-wired' organisms constrained by DNA mutation 10 . Together, the actions of reading, 'riting, 'rithmetic and replication constitute the four Rs of RNA-directed evolution. Here, we describe roles for coRNAs and SATs (Fig. 2) in these events. RNA-directed RNA readoutRNA coregulates the sequence-specific read-out of genetic information from RNA by targeting the evolutionarily conserved machinery of RNA interference (RNAi) 11 and translational repression. RNAi leading to post-transcriptional gene silencing (PTGS) is induced by doublestranded RNA (dsRNA) arising from infection by dsRNA viruses, senseantisense transcription pairs, transcription of inverted repeats and delivery of dsRNAs manufactured in vitro 12 . Both endogenous and exogenous dsRNAs are processed cytoplasmically by RNase III dicer paralogs into small interfering RNAs (siRNAs) that are 21-25 bases long 12,13 . These siRNAs are incorporated into an RNA-induced silencing complex (RISC) that targets any RNA with a sequence complementary to the siRNA 12,14 . The target RNA is cleaved by RISC, which has endonucleolytic and presumed exonucleolytic activity 12,15 . Each cycle results in the destruction of the target RNA and the regeneration of an active RISC 16,17 .In Neurospora crassa 18,19 , plants 20 , Schizosaccharomyces pombe 21 and Caenorhabditis elegans 22 , but not in flies, humans or mouse oocyctes 18,19,23,24 , PTGS can also be initiated by an RNA-dependent RNA polymerase (RdRP) that synthesizes complementary RNA from highly expressed transcripts to generate dsRNA. This process can spread from the 3´ to the 5´ end of the mRNA, leading to progressive silencing of a gene and other mRNAs with exons in common (transitive RNAi) 18,22 . From the evolutionary viewpoint, transitive RNAi favors the generation of new phenotypes, as related genes in species with polyploid genomes will escape cosuppression by sequence divergence, resulting in altered function or expression.The number of dicer paralogs also differs between species. Arabidopsis, which has at least four dicer family members, seems to use different enzymes to defend against viruses and to process endogenously produced dsRNA 13,25 . In humans, mice and worms, there is only one dicer ortholog, suggesting that any pathway-specific functions are guided by ancillary regulatory proteins associated with RISC. These ancillary proteins include me...

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Section: Rna-directed Rewriting Of Rnamentioning

confidence: 99%

The four Rs of RNA-directed evolution

Herbert

2003

Nat Genet

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“…It is estimated that >90% of human genes undergo alternative splicing 1 . The process is highly regulated 2 and disruption of the splicing regulatory networks can contribute to several diseases 3 . Regulation of alternative splicing involves cisacting regulatory elements that are bound by trans-acting factors to enhance or silence splicing of alternative exons.…”

Section: Introductionmentioning

confidence: 99%

Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs

Dominguez

Fisette

Chabot

et al. 2010

Nat Struct Mol Biol

139

174

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The heterogeneous nuclear ribonucleoprotein (hnRNP) F is involved in the regulation of mRNA metabolism by specifically recognizing G-tract RNA sequences. We have determined the solution structures of the three quasi RNA recognition motifs (qRRMs) of hnRNP F in complex with G-tract RNA. These structures show that qRRMs bind RNA in a very unusual manner, the G-tract being "encaged", making the qRRM a novel RNA binding domain. We defined a consensus signature sequence for qRRMs and identified other human qRRM-containing proteins, which also specifically recognize G-tract RNAs. Our structures explain how qRRMs can sequester G-tracts maintaining them in a single-stranded conformation. We also show that isolated qRRMs of hnRNP F are sufficient to regulate the alternative splicing of the Bcl-x premRNA strongly suggesting that hnRNP F would act by remodeling RNA secondary and tertiary structures.3

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“…22,23 Nonetheless, the mechanisms and functional significance of the process are still unclear. The IL23R gene is a recently discovered interleukin receptor, which plays a pivotal role in human autoimmune responses through Th17 pathway.…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of multiple splice forms of the human interleukin-23 receptor α chain in mitogen-activated leukocytes

Mancini

Gallagher

2008

Genes Immun

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The signalling of interleukin-23 (IL-23) and its receptor (IL-23R) is a key element in the differentiation of T cells to the Th17 phenotype. Here, we present the identification and characterization of human IL23R splice variants resulting from alternative splicing of the IL23R mRNA, from activated human leukocytes, following the analysis of IL23R cDNA. Twenty-four different IL23R transcripts were observed in this study, which may potentially lead to an alteration in the protein coding region of IL-23Ra. Consequently, by analysing amino acid sequences deduced from alternatively spliced mRNA sequences, four different putative premature early termination forms of IL-23Ra: (1) a very short 'IL-23Ra', (2) an IL-23Ra containing only the extracellular region, (3) a IL-23Ra with truncated intracellular domain and (4) in-frame exon-skipping causing changes to the extracellular region of the IL-23Ra were revealed. These changes may affect the function of IL-23R by altering the ligand-binding interaction, producing a soluble form of the receptor to act as a decoy receptor and/or modify the IL-23/IL-23R signalling, respectively. Taken together, identification of potentially functional splice variants of IL23R underscores the biological diversity of the IL23R gene and will aid in the understanding of the gene's function in normal and pathological conditions.

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Mechanisms of Alternative Pre-Messenger RNA Splicing

Cited by 2,327 publications

References 368 publications

The four Rs of RNA-directed evolution

The four Rs of RNA-directed evolution

Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs

Identification and characterization of multiple splice forms of the human interleukin-23 receptor α chain in mitogen-activated leukocytes

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