Splicing-Dependent RNA Polymerase Pausing in Yeast

Abstract

SummaryIn eukaryotic cells, there is evidence for functional coupling between transcription and processing of pre-mRNAs. To better understand this coupling, we performed a high-resolution kinetic analysis of transcription and splicing in budding yeast. This revealed that shortly after induction of transcription, RNA polymerase accumulates transiently around the 3′ end of the intron on two reporter genes. This apparent transcriptional pause coincides with splicing factor recruitment and with the first detection of spliced mRNA and is repeated periodically thereafter. Pausing requires productive splicing, as it is lost upon mutation of the intron and restored by suppressing the splicing defect. The carboxy-terminal domain of the paused polymerase large subunit is hyperphosphorylated on serine 5, and phosphorylation of serine 2 is first detected here. Phosphorylated polymerase also accumulates around the 3′ splice sites of constitutively expressed, endogenous yeast genes. We propose that transcriptional pausing is imposed by a checkpoint associated with cotranscriptional splicing.

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

“…The tri-snRNP (U4/U6 U5) joins next, and subsequent ATP-dependent RNA helicase-mediated rearrangements remove the U1 and U4 snRNPs and reorganize the remaining snRNPs to promote the 2 catalytic steps of splicing. In Saccharomyces cerevisiae, splicing takes place primarily during RNA Polymerase II (RNA Pol II) transcription [2][3][4] and studies have revealed that snRNPs assemble onto the nascent premRNA co-transcriptionally. [5][6][7][8][9] Mounting evidence supports a model in which pre-mRNA splicing is tightly coordinated with transcription to ensure precise and efficient gene expression.…”

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

“…4,8,[14][15][16] Thus, RNAPII S5P localizes to different chromatin regions, including repressed bivalent genes, 14 active promoters/promoter proximal regions 3 and at splice site junctions. 3,15 Furthermore, most of these RNAPII S5P contexts are affiliated with a pausing of RNAPII, 14,17,18 indicating that S5P is additionally important for co-transcriptional processing of pre-mRNA. Similarly, PHF13 localizes to each of these regions and interacts with RNAPII phosphorylated at serine 5 and serine 7, H3K4me2/3, PRC2 and several splicing factors 1 linking PHF13 to the various described functions of RNAPII S5P.…”

“…S5P is required for efficient co-transcriptional splicing and has been reported to be involved in spliceosome assembly at the 5 0 and 3 0 splice sites triggering a splicing checkpoint and RNAPII pausing at intron-exon junctions. [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 and other novel mutations in chronic lymphocytic leukemia and myeloid malignancies

“…The role of alternative splicing in cell differentiation has been well established and deregulation of these processes could be involved in cell transformation. 32,33 POTENTIAL CONSEQUENCES OF SPLICEOSOME MUTATIONS Splicing is often tightly coupled with transcription 34,35 and recent work suggests that alternative splicing might be affected by chromatin structure and histone modification. 35,36 Some of these effects might involve direct recruitment of splice factors by chromatin mark readers, as has been shown for MRG15 (also known as MORF4L1) binding to H3K36me3 and recruitment of the polypyrimidine tract-binding protein to the nascent mRNA.…”