Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

Saldi, Tassa; Cortázar, Michael A.; Sheridan, Ryan M.; Bentley, David L.

doi:10.1016/j.jmb.2016.04.017

Cited by 243 publications

(245 citation statements)

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“…As a result of splicing being cotranscriptional, RNA polymerase II (RNAPII) elongation rate can influence splicing. According to one model, referred to as the "kinetic coupling" model, variations in RNAPII elongation rate can alter the time available, or the "window of opportunity" for upstream splice sites to be recognized before competing downstream splice sites are produced (Roberts et al 1998;de la Mata et al 2003;Kornblihtt 2007;Naftelberg et al 2015;Saldi et al 2016). Consistent with this model, it was shown that the RNAPII elongation rate is tuned by different elongation factors and other barriers like chromatin structure, which thereby impact splicing decisions (Kornblihtt 2007;Naftelberg et al 2015;Saldi et al 2016).…”

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confidence: 95%

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

et al. 2017

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The functional consequences of alternative splicing on altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects of splicing on changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both cotranscriptional splicing and splicing efficiency and that faster elongation reduces cotranscriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when cotranscriptional. Moreover, we demonstrate that altering the RNA polymerase II elongation rate in either direction compromises splicing fidelity, and we reveal that splicing fidelity depends largely on intron length together with secondary structure and splice site score. These effects are notably stronger for the highly expressed ribosomal protein coding transcripts. We propose that transcription by RNA polymerase II is tuned to optimize the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the nonribosomal protein transcripts.[Supplemental material is available for this article.]Splicing is the process of removing introns from precursor messenger RNAs (pre-mRNAs) and joining adjacent exons to produce spliced mRNA. The excised intron, in the form of a branched lariat, is rapidly debranched and discarded. If genes contain multiple introns, alternative splicing pathways can give rise to distinct mRNA and protein isoforms by using alternative splice sites or by including or excluding particular exons. In human cells, ∼95% of transcripts are alternatively spliced, thereby greatly expanding the coding capacity of the genome (Kornblihtt et al. 2013). Moreover, alternative splicing events that introduce translational stop codons in mRNAs are generally coupled with nonsensemediated decay (NMD) to down-regulate that spliced isoform, offering an additional layer of gene expression regulation (Lewis et al. 2003;Sayani et al. 2008;Kawashima et al. 2014). In Saccharomyces cerevisiae (budding yeast) only ∼5% of genes contain an intron, although they produce ∼27% of total mRNA, because many intron-containing genes are highly expressed (Ares et al. 1999). There is extensive evidence that in both metazoans and budding yeast, the process of splicing occurs as soon as the intron is transcribed and before transcription termination, that is, cotranscriptionally (Alexander et al. 2010b;Ameur et al. 2011;Carrillo Oesterreich et al. 2016). As a result of splicing being cotranscriptional, RNA polymerase II (RNAPII) elongation rate can influence splicing. According to one model, referred to as the "kinetic coupling" model, variations in RNAPII elongation rate can alter the time available, or the "window of opportunity" for upstream splice sites to be recognized before competing downstream splice sites are produced (Roberts et al. 1998;de la Mata et al. 2003;Kornblihtt 2007;Naftelberg et al. 2015;Saldi et al. 2016). Consistent with this model, ...

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confidence: 95%

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

et al. 2017

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“…Many splicing factors (e.g., components of U1, U2, U5 RNPs, Sm, and NTC) and some polyadenylation-related proteins copurified with the TEFs. It is likely that a portion of the mRNA processing factors that is enriched in the affinity purifications of the TEFs physically interacts with the elongating RNAPII (Elkon et al, 2013;Perales and Bentley, 2009;Saldi et al, 2016). Several subunits of PAF1-C also copurified with the polyadenylation factor CstF.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, it turned out that both splicing and polyadenylation are linked to transcript elongation and that there is a close interrelationship between ongoing transcription and mRNA processing (Perales and Bentley, 2009). For example, the RNAPII elongation rate, which is under control of TEFs, influences the efficiency of splicing and polyadenylation events (Elkon et al, 2013;Saldi et al, 2016). In plants, the interplay between transcript elongation and mRNA processing has only recently become apparent, as exemplified by the connection of TFIIS and PAF1-C with splicing (Dolata et al, 2015;Li et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

et al. 2017

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Transcript elongation factors (TEFs) are a heterogeneous group of proteins that control the efficiency of transcript elongation of subsets of genes by RNA polymerase II (RNAPII) in the chromatin context. Using reciprocal tagging in combination with affinity purification and mass spectrometry, we demonstrate that in Arabidopsis thaliana, the TEFs SPT4/SPT5, SPT6, FACT, PAF1-C, and TFIIS copurified with each other and with elongating RNAPII, while P-TEFb was not among the interactors. Additionally, NAP1 histone chaperones, ATP-dependent chromatin remodeling factors, and some histone-modifying enzymes including Elongator were repeatedly found associated with TEFs. Analysis of double mutant plants defective in different combinations of TEFs revealed genetic interactions between genes encoding subunits of PAF1-C, FACT, and TFIIS, resulting in synergistic/epistatic effects on plant growth/development. Analysis of subnuclear localization, gene expression, and chromatin association did not provide evidence for an involvement of the TEFs in transcription by RNAPI (or RNAPIII). Proteomics analyses also revealed multiple interactions between the transcript elongation complex and factors involved in mRNA splicing and polyadenylation, including an association of PAF1-C with the polyadenylation factor CstF. Therefore, the RNAPII transcript elongation complex represents a platform for interactions among different TEFs, as well as for coordinating ongoing transcription with mRNA processing.

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“…[15][16][17][29][30][31] Mammalian NET-seq demonstrated RNAPII S5P enrichment at 5 0 and 3 0 splice sites 15 and phospho-specific RNAPII immunoprecipitations have revealed that RNAPII S5P interacts with key proteins involved spliceosomal assembly. 15,16,29 For a detailed reviews on co-transcriptional splicing, we refer the reader to Saldi et al (2016) and Jonkers et al (2015) 25,32 . Spliceosome assembly is a multi-step process that occurs on the pre-mRNA transcript, starting with recruitment of U1 snRNP at the 5 0 splice site 33 and U2 snRNP to the exonic nucleosome at the 3SS 34 and then at the branch point to form the pre-spliceosome (complex A).…”

Section: Splicing Checkpointmentioning

confidence: 99%

PHF13: A new player involved in RNA polymerase II transcriptional regulation and co-transcriptional splicing

2017

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We recently identified PHF13 as an H3K4me2/3 chromatin reader and transcriptional co-regulator. We found that PHF13 interacts with RNAPIIS5P and PRC2 stabilizing their association with active and bivalent promoters. Furthermore, mass spectrometry analysis identified »50 spliceosomal proteins in PHF13s interactome. Here, we will discuss the potential role of PHF13 in RNAPII pausing and co-transcriptional splicing.

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Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

Cited by 243 publications

References 165 publications

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

PHF13: A new player involved in RNA polymerase II transcriptional regulation and co-transcriptional splicing

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