Role and mechanism of U1-independent pre-mRNA splicing in the regulation of alternative splicing

Fukumura, Kazuhiro; Inoue, Kimiko

doi:10.4161/rna.6.4.9318

Cited by 9 publications

(7 citation statements)

References 25 publications

(29 reference statements)

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“…Although spliceosome assembly in human extracts is similarly blocked by degrading U2 snRNA(Krainer and Maniatis, 1985), human extracts supplemented with SR proteins are capable of splicing even in the absence of U1 snRNP(Crispino et al, 1994; Konforti et al, 1993; Tarn and Steitz, 1994). This difference between the yeast and mammalian systems likely reflects additional positive interactions in the mammalian system between the core splicing machinery and non-snRNP splicing factors bound to exonic and intronic splicing enhancer (ESE and ISE) elements (reviewed in (Fukumura and Inoue, 2009; Roca et al, 2013)).…”

Section: Discussionmentioning

confidence: 99%

Alternative Spliceosome Assembly Pathways Revealed by Single-Molecule Fluorescence Microscopy

Shcherbakova¹,

Hoskins²,

Friedman³

et al. 2013

Cell Reports

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SUMMARY Removal of introns from nascent transcripts (pre-mRNAs) by the spliceosome is an essential step in eukaryotic gene expression. Previous studies have suggested that the earliest steps in spliceosome assembly in yeast are highly ordered, with stable recruitment of U1 snRNP to the 5' splice site necessarilypreceding recruitment of U2 snRNP to the branch site to form the “pre-spliceosome”. Using Colocalization Single Molecule Spectroscopy (CoSMoS) to follow initial spliceosome assembly on eight different S. cerevisiae pre-mRNAs, we here demonstrate that active yeast spliceosomes can form by both U1-first and U2-first pathways. Both assembly pathways yield prespliceosomes functionally equivalent for subsequent U5•U4/U6 tri-snRNP recruitment and for intron excision. Although fractional flux through the two pathways varies on different introns, both are operational on all introns studied. Thus, multiple pathways exist toassemble functional spliceosomes. These observations provide new insight into the mechanisms of cross-intron coordination of initial spliceosome assembly.

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Section: Discussionmentioning

confidence: 99%

Alternative Spliceosome Assembly Pathways Revealed by Single-Molecule Fluorescence Microscopy

Shcherbakova¹,

Hoskins²,

Friedman³

et al. 2013

Cell Reports

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“…Similar cross-exon regulation of intron excision has been reported for alternative splicing regulation of exon 9 of the human ATP5C1 gene encoding mitochondrial ATP synthase γ subunit, where RBFOX1 represses excision of intron 9 by binding to GCAUG stretches in intron 8 to interfere with E complex formation on intron 9 (58). Interestingly, ATP5C1 intron 9 has been shown to be excised by U1-independent U2-type splicing which contributes to alternative splicing regulation although the molecular mechanism is to be elucidated (59,60). Genome-wide analysis of PTBP1–RNA interactions suggested that binding of PTBP1 near the constitutive 3′-splice site of the downstream introns interferes with the recognition of the constitutive 3′-splice site to promote the use of the alternative exons (61).…”

Section: Discussionmentioning

confidence: 99%

Position-dependent and neuron-specific splicing regulation by the CELF family RNA-binding protein UNC-75 in Caenorhabditis elegans

Kuroyanagi

Watanabe

Suzuki

et al. 2013

Nucleic Acids Research

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A large fraction of protein-coding genes in metazoans undergo alternative pre-mRNA splicing in tissue- or cell-type-specific manners. Recent genome-wide approaches have identified many putative-binding sites for some of tissue-specific trans-acting splicing regulators. However, the mechanisms of splicing regulation in vivo remain largely unknown. To elucidate the modes of splicing regulation by the neuron-specific CELF family RNA-binding protein UNC-75 in Caenorhabditis elegans, we performed deep sequencing of poly(A)+ RNAs from the unc-75(+)- and unc-75-mutant worms and identified more than 20 cassette and mutually exclusive exons repressed or activated by UNC-75. Motif searches revealed that (G/U)UGUUGUG stretches are enriched in the upstream and downstream introns of the UNC-75-repressed and -activated exons, respectively. Recombinant UNC-75 protein specifically binds to RNA fragments carrying the (G/U)UGUUGUG stretches in vitro. Bi-chromatic fluorescence alternative splicing reporters revealed that the UNC-75-target exons are regulated in tissue-specific and (G/U)UGUUGUG element-dependent manners in vivo. The unc-75 mutation affected the splicing reporter expression specifically in the nervous system. These results indicate that UNC-75 regulates alternative splicing of its target exons in neuron-specific and position-dependent manners through the (G/U)UGUUGUG elements in C. elegans. This study thus reveals the repertoire of target events for the CELF family in the living organism.

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“…U1-independent splicing may be an example that supports this explanation [47,48]. Although the detailed mechanism of U1-independent splicing is unclear and further research is needed, hF1γ intron 9, whose 5' splice site sequences are different from the consensus sequence at positions -3 and +5, spliced out without U1 snRNP.…”

Section: Discussionmentioning

confidence: 99%

A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing

et al. 2010

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BackgroundAlternative splicing (AS) is a key molecular process that endows biological functions with diversity and complexity. Generally, functional redundancy leads to the generation of new functions through relaxation of selective pressure in evolution, as exemplified by duplicated genes. It is also known that alternatively spliced exons (ASEs) are subject to relaxed selective pressure. Within consensus sequences at the splice junctions, the most conserved sites are dinucleotides at both ends of introns (splice dinucleotides). However, a small number of single nucleotide polymorphisms (SNPs) occur at splice dinucleotides. An intriguing question relating to the evolution of AS diversity is whether mutations at splice dinucleotides are maintained as polymorphisms and produce diversity in splice patterns within the human population. We therefore surveyed validated SNPs in the database dbSNP located at splice dinucleotides of all human genes that are defined by the H-Invitational Database.ResultsWe found 212 validated SNPs at splice dinucleotides (sdSNPs); these were confirmed to be consistent with the GT-AG rule at either allele. Moreover, 53 of them were observed to neighbor ASEs (AE dinucleotides). No significant differences were observed between sdSNPs at AE dinucleotides and those at constitutive exons (CE dinucleotides) in SNP properties including average heterozygosity, SNP density, ratio of predicted alleles consistent with the GT-AG rule, and scores of splice sites formed with the predicted allele. We also found that the proportion of non-conserved exons was higher for exons with sdSNPs than for other exons.ConclusionssdSNPs are found at CE dinucleotides in addition to those at AE dinucleotides, suggesting two possibilities. First, sdSNPs at CE dinucleotides may be robust against sdSNPs because of unknown mechanisms. Second, similar to sdSNPs at AE dinucleotides, those at CE dinucleotides cause differences in AS patterns because of the arbitrariness in the classification of exons into alternative and constitutive type that varies according to the dataset. Taking into account the absence of differences in sdSNP properties between those at AE and CE dinucleotides, the increased proportion of non-conserved exons found in exons flanked by sdSNPs suggests the hypothesis that sdSNPs are maintained at the splice dinucleotides of newly generated exons at which negative selection pressure is relaxed.

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Role and mechanism of U1-independent pre-mRNA splicing in the regulation of alternative splicing

Cited by 9 publications

References 25 publications

Alternative Spliceosome Assembly Pathways Revealed by Single-Molecule Fluorescence Microscopy

Alternative Spliceosome Assembly Pathways Revealed by Single-Molecule Fluorescence Microscopy

Position-dependent and neuron-specific splicing regulation by the CELF family RNA-binding protein UNC-75 in Caenorhabditis elegans

A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing

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