Recursive splicing in long vertebrate genes

Sibley, Christopher R.; Emmett, Warren; Blázquez, Lorea; Faro, Ana; Haberman, Nejc; Briese, Michael; Trabzuni, Daniah; Ryten, Mina; Weale, Michael E.; Hardy, John; Modic, Miha; Curk, Tomaž; Wilson, Stephen W.; Plagnol, Vincent; Ule, Jernej

doi:10.1038/nature14466

Cited by 146 publications

(297 citation statements)

References 31 publications

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“…In the second step, splicing from a 59 splice site either at the start of the cassette exon or downstream of it results in removal and inclusion of the cassette exon, respectively. Like SR30.3, most of the cassette exon variants resulting from recursive splicing in vertebrate genes are targeted by NMD (Sibley et al, 2015). Interestingly, the regulated intron in SR30 and the corresponding introns from other SR genes showing SR30-like AS patterns are exceptionally long, with 942 nucleotides for SR30 and ranging from 765 to 1100 nucleotides for the other cases (Supplemental Fig.…”

Section: Possible Alternative Routes For the Generation Of The Sr303mentioning

confidence: 99%

“…Recently, further examples of recursive splicing events, involving generation of zero nucleotide exons, have been described for D. melanogaster (Duff et al, 2015). Identification of recursive splicing in vertebrate genes (Sibley et al, 2015) demonstrated that this mechanism is not restricted to D. melanogaster. Interestingly, all of the recursive splicing events found in human can result in cassette exon inclusion (CookAndersen and Wilkinson, 2015;Sibley et al, 2015), equivalent to the proposed consecutive splicing events resulting in SR30.3.…”

Section: Possible Alternative Routes For the Generation Of The Sr303mentioning

confidence: 99%

“…Identification of recursive splicing in vertebrate genes (Sibley et al, 2015) demonstrated that this mechanism is not restricted to D. melanogaster. Interestingly, all of the recursive splicing events found in human can result in cassette exon inclusion (CookAndersen and Wilkinson, 2015;Sibley et al, 2015), equivalent to the proposed consecutive splicing events resulting in SR30.3. In the first step, the intron upstream of the cassette exon is spliced out.…”

Section: Possible Alternative Routes For the Generation Of The Sr303mentioning

confidence: 99%

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Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

2018

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Alternative splicing (AS) is prevalent in higher eukaryotes, and generation of different AS variants is tightly regulated. Widespread AS occurs in response to altered light conditions and plays a critical role in seedling photomorphogenesis, but despite its frequency and effect on plant development, the functional role of AS remains unknown for most splicing variants. Here, we characterized the light-dependent AS variants of the gene encoding the splicing regulator Ser/Arg-rich protein SR30 in Arabidopsis (Arabidopsis thaliana). We demonstrated that the splicing variant SR30.2, which is predominantly produced in darkness, is enriched within the nucleus and strongly depleted from ribosomes. Light-induced AS from a downstream 39 splice site gives rise to SR30.1, which is exported to the cytosol and translated, coinciding with SR30 protein accumulation upon seedling illumination. Constitutive expression of SR30.1 and SR30.2 fused to fluorescent proteins revealed their identical subcellular localization in the nucleoplasm and nuclear speckles. Furthermore, expression of either variant shifted splicing of a genomic SR30 reporter toward SR30.2, suggesting that an autoregulatory feedback loop affects SR30 splicing. We provide evidence that SR30.2 can be further spliced and, unlike SR30.2, the resulting cassette exon variant SR30.3 is sensitive to nonsense-mediated decay. Our work delivers insight into the complex and compartmentalized RNA processing mechanisms that control the expression of the splicing regulator SR30 in a light-dependent manner.Maturation of eukaryotic mRNAs involves intricate co-and posttranscriptional RNA processing, which has critical functions in regulating gene expression and diversifying the transcriptome. Among several mechanisms, alternative precursor mRNA splicing (AS) in particular generates many transcript variants by removing distinct intronic regions and joining the resulting exons. Deep analysis of transcriptomes via high-throughput RNA sequencing (RNA-seq) has revealed that a major fraction of all intron-containing genes from higher eukaryotes generates AS variants. In humans, more than 95% of multiexon genes display AS (Pan et al., 2008). The prevalence of AS has also been demonstrated for other eukaryotes including plants (Reddy et al., 2013;Staiger and Brown, 2013), with current estimates of ;61% and ;42% of intron-containing genes giving rise to AS variants in the model plants Arabidopsis (Arabidopsis thaliana;Marquez et al., 2012) and Brachypodium distachyon (Mandadi and Scholthof, 2015), respectively.Besides its pivotal role in increasing the coding and regulatory capacity of the transcriptome, AS finetunes gene expression by varying the output ratios of splicing variants. The full extent of AS regulation likely exceeds the current estimates, as the production of many transcript variants can be specifically controlled under certain conditions, such as cell and tissue types, developmental stages, and in response to stresses and other environmental factors (Reddy et al., 2013;Staige...

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Section: Possible Alternative Routes For the Generation Of The Sr303mentioning

confidence: 99%

Section: Possible Alternative Routes For the Generation Of The Sr303mentioning

confidence: 99%

Section: Possible Alternative Routes For the Generation Of The Sr303mentioning

confidence: 99%

See 1 more Smart Citation

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

2018

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“…First, LITseq, unlike other intron probing approaches, can be adapted to define 3 ′ splice sites, by targeting the 3 ′ termini of excised but intact introns. By defining 5 ′ splice sites, branch sites, and 3 ′ splice sites, LIT-seq would not only allow the empirical annotation of introns but would also have the potential to reveal recursive splicing events, in which the spliceosome excises large introns by sequentially removing nested introns (Hatton et al 1998;Lopez and Séraphin 2000;Sibley et al 2015;Duff et al 2015). While the fully processed mRNA product cannot distinguish between intron excision in a single step from excision in multiple recursive steps, the intron products resulting from these two alternative pathways do distinguish between these mechanisms, because the lariats effectively record each splicing event.…”

Section: Future Applications Of Lit-seqmentioning

confidence: 99%

Sequencing of lariat termini in S. cerevisiae reveals 5′ splice sites, branch points, and novel splicing events

Qin

Huang

Wlodaver

et al. 2015

RNA

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Pre-mRNA splicing is a central step in the shaping of the eukaryotic transcriptome and in the regulation of gene expression. Yet, due to a focus on fully processed mRNA, common approaches for defining pre-mRNA splicing genome-wide are suboptimalespecially with respect to defining the branch point sequence, a key cis-element that initiates the chemistry of splicing. Here, we report a complementary intron-centered approach designed to more efficiently, simply, and directly define splicing events genome-wide. Specifically, we developed a method distinguished by deep sequencing of lariat intron termini (LIT-seq). In a test of LIT-seq using the budding yeast Saccharomyces cerevisiae, we not only successfully captured the majority of annotated, expressed splicing events but also uncovered 45 novel splicing events, establishing the sensitivity of LIT-seq. Moreover, our libraries were highly enriched with reads that reported on splice sites; by a simple and direct inspection of sequencing reads, we empirically defined both 5 ′ splice sites and branch sites, as well as their consensus sequences, with nucleotide resolution. Additionally, our study revealed that the 3 ′ termini of lariat introns are subject to nontemplated addition of adenosines, characteristic of signals sensed by 3 ′ to 5 ′ RNA turnover machinery. Collectively, this work defines a novel, genome-wide approach for analyzing splicing with unprecedented depth, specificity, and resolution.

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“…Duff et al 5 report that this recursive splicing process occurs in the fruit fly Drosophila melanogaster much more commonly than was previously thought. b, Sibley et al 6 find that some recursively spliced messenger RNAs -including all those known in humans -contain a recursive splicing (RS) exon. The RS exon can be either completely removed or retained in the mature mRNA, depending on which of two competing 5ʹ splice sites is used in the second step.…”

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confidence: 99%

Correction: Clarification

2015

Nature

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Recursive splicing in long vertebrate genes

Cited by 146 publications

References 31 publications

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression

Sequencing of lariat termini in S. cerevisiae reveals 5′ splice sites, branch points, and novel splicing events

Correction: Clarification

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