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Tyrosine-1 of RNA polymerase II CTD controls global termination of gene transcription in mammals

ABSTRACT: The aim of the project was to analyse the functional role of Tyrosine-1 of mammalian RNA polymerase II CTD in the regulation of transcription-coupled processes. We studied mammalian CTD mutants to analyze the function of tyrosine1 residues. Mutation of 3/4 of the tyrosine residues in a mutant YFFF resulted in a massive read-through transcription phenotype. Read-through was observed for 3’ processed and polyadenylated RNAs. The YFFF mutant shows a loss of interaction with the Mediator and Integrator complexes in MS analysis.

OTHER RELATED OMICS DATASETS IN: PRJNA369388

INSTRUMENT(S): LTQ Orbitrap, Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Ignasi Forne

LAB HEAD: Prof. Dr. Dirk Eick

PROVIDER: PXD008270 | Pride | 2018-01-09

REPOSITORIES: pride

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			Action	DRS
	MS_rWTandYFFFmutants.xlsx	Xlsx
	Proteingroups_IF_20160919_NS.xlsx	Xlsx
	Ref547_NS_WTrec_150212.raw	Raw
	Ref547_NS_YF3_150212.raw	Raw
	Ref620_NS_WTrec_bead_160122.raw	Raw

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Tyrosine-1 of RNAPII CTD controls global termination of gene transcription in mammals

Project description:The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is composed of a repetition of YSPTSPS heptads and functions as a loading platform for protein complexes that regulate transcription, splicing and maturation of RNAs. Here, we studied mammalian CTD mutants to analyze the function of tyrosine1 residues in the transcription cycle. Mutation of 3/4 of the tyrosine residues (YFFF mutant) resulted in a massive read-through transcription phenotype in antisense direction of promoters as well as in 3' direction several hundred kb downstream of genes. The YFFF mutant shows reduced Pol II at promoter-proximal pause sites, a loss of interaction with the Mediator and Integrator complexes and impaired recruitment of these complexes to chromatin. Consistent with these observations, Pol II loading at enhancers and maturation of snRNAs are altered in the YFFF context genome wide. We conclude that tyrosine1 residues of the CTD control termination of transcription by Pol II.

2017-12-29 | GSE94330 | GEO

RNA Polymerase II CTD is dispensable for transcription in vivo and required for termination

Project description:The largest subunit of RNA polymerase (Pol) II harbors a evolutionary conserved C-Terminal-Domain (CTD), composed of a repetition of heptapeptides, central in the transcriptional process. Here, we have analysed the transcriptional phenotypes of a CTD-∆5 mutant that carries a large CTD truncation. Unexpectedly, our results indicate that this mutant can widely transcribe genes in living cells but displays an extreme pervasive phenotype with severely impaired termination, similar to but more severely impaired than previously characterized mutations of CTD tyrosine residues. The CTD-∆5 mutant has also lost its interactions with the Mediator and Integrator complexes involved in activation of transcription and maturation of RNAs. Examination of long-distance interactions and CTCF binding pattern in CTD-∆5 did not indicate major changes in TAD domains or borders. Our data demonstrate that the CTD is largely dispensable for the act of transcription per se in living cells. We propose a model in which CTD-depleted Pol II has a lower entry rate into DNA but becomes extremely pervasive once engaged in transcription, resulting in a global loss of termination.

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RNA polymerase II termination involves CTD tyrosine dephosphorylation by CPF subunit Glc7

Project description:At the 3'-ends of genes, RNA polymerase (Pol) II is dephosphorylated at tyrosine 1 residues of its C-terminal domain (CTD), resulting in recruitment of transcription termination factors. We show that the multisubunit cleavage and polyadenylation factor (CPF) is a Pol II CTD phosphatase and its Glc7 subunit is required for Tyr1 dephosphorylation at the poly-adenylation site and Pol II termination in vivo. ChIP-chip was performed to examine the effect of Glc7 nuclear depletion on genome-wide Pol II occupancy [using ?-Rpb3 (1Y26, cat. no. W0012, neoclone) antibody] and CTD tyrosine 1 phosphorylation levels [using ?-TyrY1P (3D12, D. Eick) antibody].

2013-12-16 | E-MTAB-1528 | biostudies-arrayexpress

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.

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Site-specific methylation and acetylation of lysine residues in the C-terminal domain (CTD) of RNA polymerase II

Project description:Dynamic modification of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) regulates transcription-coupled processes in eukaryotes. The CTD in mammals is composed of 52 heptad-repeats with the consensus sequence Y1-S2-P3-T4-S5-P6-S7. Repeats in the distal part of CTD deviate from the consensus sequence and have frequently replaced serine at position 7 by lysine residues (K7). Mass spectrometry analysis revealed modification of K7 residues in heptad-repeats 39, 42, and 47/49 by acetylation and in heptad-repeats 38, 39, 40, 42, and 47/49 by mono-, di-, or trimethylation. Notably, acetylated as well as di- and tri-methylated K7 residues were found exclusively in phosphorylated CTD peptides, while mono-methylated K7 residues occurred also in non-phosphorylated CTD peptides. Methylation of K7 residues was further studied with the monoclonal antibody (mAb) 1F5, which recognizes mono- and di-methylated K7 in CTD. ChIP experiments revealed high levels of K7 methylation at the transcriptional start site of genes. The low levels of K7 methylation in the body of genes results from impairment of epitope recognition in hyper-phosphorylated CTD by mAb 1F5. In agreement with this notion, phosphatase treatment of hyper-phosphorylated CTD or treatment of cells with kinase inhibitor flavopiridol restored the reactivity of mAb 1F5 towards methylated K7 residues in CTD. We conclude that methylation and acetylation of K7 residues further expand the mammalian CTD code and potentially contribute to regulation of gene expression.

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Project description:The carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) consists of heptad repeats with the consensus motif Y1-S2-P3-T4-S5-P6-S7. Dynamic phosphorylation of the CTD coordinates Pol II progression through the transcription cycle. Monoclonal antibodies have been used to study in vivo the potentially phosphorylated CTD amino acids (Y1, S2, T4, S5 and S7). However, the epitopes detected by antibodies can be masked by proteins or modifications at neighbouring sites. Therefore, the effectiveness of antibodies in western blot or ChIP analysis reflects the number of accessible CTD phosphorylation marks, but not the total number of phosphorylations. Most importantly, CTD phospho-specific antibodies do not provide any heptad - (location) specific information of CTD phosphorylation. Due to these limitations, the principles and patterns of CTD phosphorylation remained elusive. Here, we use genetic and mass spectrometric approaches to directly detect and map phosphosites along the entire CTD. We confirm phosphorylation of CTD residues Y1, S2, T4, S5 and S7 in mammalian and yeast cells. Although specific phosphorylation signatures dominate, adjacent CTD repeats can be differently phosphorylated, leading to a high variation of coexisting phosphosites in mono- and di-heptad CTD repeats. Inhibition of CDK9 kinase specifically reduces S2 phosphorylation levels within the CTD.

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Project description:The carboxy-terminal domain (CTD) of the largest subunit of RNA Polymerase II (RNAPII) consists of multiple tandem repeats of the heptapeptide consensus Y1-S2-P3-T4-S5-P6-S7. RNAPII CTD is intrinsically disordered and has been shown to promote liquid-liquid phase-separation (LLPS) of RNAPII in vivo. However, understanding the precise role of the conserved heptad residues in LLPS has been hampered by the lack of direct characterization of the biochemical properties of the CTD. Here, we generated a systematic array of RNAPII CTD variants to unravel the sequence-encoded molecular grammar underlying LLPS of the human CTD.

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