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Spliceosome specifically associates with RNA polymerase II CTD Ser5-P isoform to promote co-transcriptional splicing

ABSTRACT: Spliceosome specifically associates with RNA polymerase II CTD Ser5-P isoform to promote co-transcriptional splicing

PROVIDER: PRJNA418318 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6290100_1.fastq.gz	Fastqsanger.gz
	SRR6290100_2.fastq.gz	Fastqsanger.gz
	SRR6290110_1.fastq.gz	Fastqsanger.gz
	SRR6290110_2.fastq.gz	Fastqsanger.gz
	SRR6290120_1.fastq.gz	Fastqsanger.gz

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Spliceosome specifically associates with RNA polymerase II CTD Ser5-P isoform to promote co-transcriptional splicing

Project description:Co-transcriptional splicing of introns is a defining feature of eukaryotic gene expression. We show that the mammalian spliceosome specifically associates with the S5P CTD isoform of RNA polymerase II (Pol II) as it elongates across spliced exons of protein coding genes, both in human Hela and murine lymphoid cell lines. Immuno-precipitation of MNase digested chromatin with phospho CTD specific antibodies reveals that components of the active spliceosome (both snRNA and proteins) form a specific complex with S5P CTD Pol II. Furthermore a dominant splicing intermediate formed by cleavage at intron 5’ss results in the tethering of upstream exons to this complex at all spliced exons. These are invariably connected to upstream spliced constitutive and less frequently to alternative exons. Finally S5P CTD Pol II accumulates over spliced exons but not adjacent introns. We propose that mammalian splicing employs a rapid, co-transcriptional splicing mechanism based on CTD phosphorylation transitions.

2018-10-06 | GSE106881 | GEO

Spliceosome specifically associates with CTD phospho-serine 5 isoform of RNA polymerase II to promote co-transcriptional splicing

2018-10-05 | PXD008197 | Pride

PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [ChIP-seq]

Project description:The restrictor complex, WDR82/ZC3H4, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism of action is poorly understood. We report that the PP1 phosphatase nuclear targeting subunit PNUTS binds to restrictor via its WDR82 subunit. AlphaFold predicts a quaternary complex, PPWZ, in which PP1-associated PNUTS and ZC3H4 both contact WDR82. A chimera comprising inactive PP1H66K fused to the C-terminal PNUTS sequences including its WDR82 binding domain binds to restrictor and acts as a dominant negative inhibitor of antisense termination and CTD Ser5 dephosphorylation. The PP1H66K-PNUTS is a substrate trap that also interacts with pol II large subunit and nuclear exosome components. Ser5 hyperphosphorylated pol II has increased processivity and pauses less frequently than total pol II. We speculate that the elevated elongation efficiency of Ser5-P pol II antagonizes early termination and that Ser5 dephosphorylation by PP1/PNUTS/WDR82/ZC3H4 is coupled to termination of antisense transcription.

2025-04-05 | GSE269359 | GEO

PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [eNET-seq]

2025-04-05 | GSE269358 | GEO

PP1 PNUTS binds the “restrictor” and dephosphorylates pol II CTD Ser5 to stimulate RNA pol II transcription termination [nascent RNA-seq]

Project description:The restrictor complex, WDR82/ZC3H4, is the major termination factor for antisense transcription from bidirectional promoters, but its mechanism of action is poorly understood. We report that the PP1 phosphatase nuclear targeting subunit PNUTS binds to restrictor via its WDR82 subunit. AlphaFold predicts a quaternary complex, PPWZ, in which PP1-associated PNUTS and ZC3H4 both contact WDR82. A chimera comprising inactive PP1H66K fused to C-terminal PNUTS sequences is a dominant-negative inhibitor of antisense termination and CTD Ser5 dephosphorylation and both activities require the PNUTS WDR82 binding domain. PP1H66K-PNUTS is a substrate trap that also interacts with pol II large subunit and nuclear exosome components. Ser5 hyperphosphorylated pol II has increased processivity and pauses less frequently than total pol II. We propose that the elevated elongation efficiency of Ser5-P pol II antagonizes early termination and that Ser5 dephosphorylation by PP1/PNUTS/WDR82/ZC3H4 is coupled to termination of antisense transcription.

2025-04-05 | GSE269357 | GEO

RNA expression analysis in RNA Pol II CTD mutants

Project description:The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific “readers.” While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we investigate the RNA expression profile in WT and CTD-mutant strains of S. cerevisiae.

2017-05-02 | GSE95417 | GEO

Budding yeast RNA polymerase II CTD phosphorylation and transcription termination factor localization

Project description:Whole genome analysis of total RNA pol II, Ser2-, Ser5- and Ser7-phosphorylated RNA pol II, in WT and mutants of the C-terminal domain (CTD) kinases Ctk1 and Kin28, and localization of the termination factors Pcf11, Nrd1 and Rat1.

2010-09-15 | GSE23960 | GEO

CTD tyrosine phosphorylation impairs termination factor recruitment to transcribing RNA polymerase II

Project description:ChIP-chip was performed to identify the genomic binding locations for the termination factors Nrd1, and Rtt103, and for RNA polymerase (Pol) II phosphorylated at the tyrosine 1 and threonine 4 position of its C-terminal domain (CTD). In different phases of the transcription cycle, Pol II recruits different factors via its CTD, which consists of heptapeptide repeats with the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Here we show that the CTD of transcribing yeast Pol II is phosphorylated at Tyr1, and that this impairs recruitment of termination factors. Tyr1 phosphorylation levels rise downstream of the transcription start site (TSS), and decrease before the polyadenylation (pA) site. Tyr1-phosphorylated gene bodies are depleted of CTD-binding termination factors Nrd1, Pcf11, and Rtt103. Tyr1 phosphorylation blocks CTD binding by these termination factors, but stimulates binding of elongation factor Spt6. These results show that CTD modifications can not only stimulate but also block factor recruitment, and lead to an extended CTD code for transcription cycle coordination.

2012-06-29 | E-MTAB-1060 | biostudies-arrayexpress

Modification of C-terminal Domain (CTD) of RPB1 plays a role in transcriptome change upon salt stress

Project description:Transctriptome profiling of CTD-14 repeats, 2A, 5A mutants responding to 0.7N NaCl for 30mins. The study shows that phosphorylation at Ser5 sites plays a role in normal induction and repression of genes upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. 5A strains carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with Ala followed by 7 wild-type-sequenced repeats. The 2A strains carrys 8 repeats of CTD-serine 2 substituted with alanine followed by 7 wild-type-sequenced repeats.

2014-12-03 | GSE60700 | GEO

Modification of C-terminal Domain (CTD) of RPB1 plays a role in transcriptome change upon salt stress

2014-12-03 | E-GEOD-60700 | biostudies-arrayexpress