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Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain required for efficient transcription of heat shock genes

ABSTRACT: RNA polymerase II is decreased on heat shock-induced genes when the CTD phosphatase Fcp1 is knocked down in Drosophila S2 cells. We examined transcriptionally-engaged Pol II genome-wide with GRO-seq to determine if other genes are similarly affected.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE38748 | GEO | 2012/06/29

SECONDARY ACCESSION(S): PRJNA168561

REPOSITORIES: GEO

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Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain required for efficient transcription of heat shock genes

Project description:RNA polymerase II is decreased on heat shock-induced genes when the CTD phosphatase Fcp1 is knocked down in Drosophila S2 cells. We examined transcriptionally-engaged Pol II genome-wide with GRO-seq to determine if other genes are similarly affected. Two biological replicates of nascent RNA sequencing

2012-06-28 | E-GEOD-38748 | biostudies-arrayexpress

TOX4 Facilitates Promoter-Proximal Pausing and C-Terminal Domain Dephosphorylation of RNA Polymerase II in Human Cells

Project description:TOX4 is one of the regulatory proteins of PP1 phosphatases with poorly understood functions. Here we show that chromatin occupancy pattern of TOX4 resembles that of RNA polymerase II (Pol II), and its loss increases cellular level of C-terminal domain (CTD) phosphorylated Pol II but mainly decreases Pol II occupancy on promoters. In addition, elongation rate analyses by 4sUDRB-seq suggest that TOX4 restricts pause release and early elongation but promotes late elongation. Moreover, TT-seq analyses indicate that TOX4 loss mainly decreases transcriptional output. Mechanistically, TOX4 may restrict pause release through facilitating CTD serine 2 and DSIF dephosphorylation, and promote Pol II recycling and reinitiation through facilitating CTD serines 2 and 5 dephosphorylation. Furthermore, among the PP1 phosphatases, TOX4 preferentially binds PP1α and is capable of facilitating Pol II CTD dephosphorylation in vitro. These results lay the foundation for a better understanding of the role of TOX4 in transcriptional regulation.

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Distribution of RNA polymerase II and changes of carbo-terminal phosphorylation sites after INTS11 knockdown

Project description:As Integrator is tightly associated with RNAPII-CTD, it is critical to understand how the RNAPII engaged and conducted within the active gene promoter for divergent transcription. We thus employed RNAPII ChIP-seq (Chromatin Immuno-precipitation with RNAPII antibody) to determine the distribution of the total RNAPII and its phosphorylation isoforms. Total RNA polymerase II and its carbon terminal phosphorylation(RNA polymerase II-ctd-Tyr-1，RNA polymerase II-ctd-ser-2) before and after INTS11 knockdown in HCT116-INTS11-AID cells changes chromatin immunoprecipitation DNA sequencing (ChIP-seq).

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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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CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

Project description:Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.

2020-06-18 | GSE133156 | GEO

CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

2020-06-03 | GSE115290 | GEO

Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain is required for efficient transcription of heat shock genes.

Project description:Fcp1 dephosphorylates the C-terminal domain of the largest subunit of RNA polymerase II (Pol II) to recycle it into a form that can initiate a new round of transcription. Previously, we identified Drosophila Fcp1 as an important factor in optimal Hsp70 mRNA accumulation after heat shock. Here, we examine the role of Fcp1 in transcription of heat shock genes in vivo. We demonstrate that Fcp1 localizes to active sites of transcription including the induced Hsp70 gene. The reduced Hsp70 mRNA accumulation seen by RNA interference (RNAi) depletion of Fcp1 in S2 cells is a result of a loss of Pol II in the coding region of highly transcribed heat shock-induced genes: Hsp70, Hsp26, and Hsp83. Moreover, Fcp1 depletion dramatically increases phosphorylation of the non-chromatin-bound Pol II. Reexpression of either wild-type or catalytically dead versions of Fcp1 demonstrates that both the reduced Pol II levels on heat shock genes and the increased levels of phosphorylated free Pol II are dependent on the catalytic activity of Fcp1. Our results indicate that Fcp1 is required to maintain the pool of initiation-competent unphosphorylated Pol II, and this function is particularly important for the highly transcribed heat shock genes.

| S-EPMC3421999 | biostudies-literature

Heptad-specific phosphorylation of RNA polymerase II CTD

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.

2016-01-25 | PXD003159 | Pride

Elf1 promotes TC-NER in yeast by using its C-terminal domain to bind TFIIH

Project description:Transcription coupled-nucleotide excision repair (TC-NER) repairs DNA lesions that stall RNA polymerase II (Pol II) transcription. Here, we show that the C-terminal domain (CTD) of elongation factor-1 (Elf1) plays a critical role in TC-NER in yeast. Analysis of genome-wide repair of UV-induced cyclobutane pyrimidine dimers (CPDs) using CPD-seq indicates that the Elf1 CTD is required for efficient Rad26-dependent and Rad26-independent TC-NER across the yeast genome. The Elf1-CTD is also important for TC-NER in rad16∆ cells deficient in GG-NER. Finally, we show that a mutant in the Elf1-CTD (elf1-Y99A) that disrupts binding to a subunit of TFIIH affects Rad26-independent repair in a rad26∆ mutant background.

2024-05-31 | GSE243603 | GEO

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

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