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FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation

ABSTRACT: We utilize the FeaSion (Feature-Screening-Function) strategy to investigate five known phosphorylation states (pY1, pS2, pT4, pS5, pS7) of RNAPII. Our study demonstrates that mutations at these phosphorylation sites broadly influence transcriptional and co-transcriptional processes. And regulators of these sites involve various biological processes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE287317 | GEO | 2025/10/28

REPOSITORIES: GEO

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FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation

Project description:We utilize the FeaSion (Feature-Screening-Function) strategy to investigate five known phosphorylation states (pY1, pS2, pT4, pS5, pS7) of RNAPII. Our study demonstrates that mutations at these phosphorylation sites broadly influence transcriptional and co-transcriptional processes. And regulators of these sites involve various biological processes.

2025-10-28 | GSE287316 | GEO

FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation

2025-10-28 | GSE287315 | GEO

FeaSion Uncovers the Multifaceted Co-transcriptional Roles of RNAPII CTD Phosphorylation Regulated by Cancer Hallmark Genes

Project description:The phosphorylation of RNAPII's C-terminal domain (CTD) has been extensively studied, yet functional investigations into all five known phosphorylation states (pY1, pS2, pT4, pS5, pS7) simultaneously are scarce, and the number of identified regulators is limited. Utilizing the FeaSion (Feature-Screening-Function) strategy, we characterized RNAPII CTD phosphorylation by identifying 706 interactors across these five states. Additionally, we conducted a CRISPR-FACS screen, revealing 2,067 potential regulators, which include 79 cancer hallmark genes, 94 kinases, and 21 phosphatases. Our study demonstrates that mutations at these phosphorylation sites broadly influence various transcriptional processes and preferentially alter co-transcriptional events, including histone modifications (H3K36me3, H2AZ, H2AZ.ac) and RNA splicing. This work offers a comprehensive perspective on RNAPII CTD phosphorylation and its regulatory network, presenting a valuable resource for future research in developmental biology and disease mechanisms.

2025-01-10 | PXD059705 |

FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-10-28 | GSE287535 | GEO

FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation

Project description:FeaSion Decodes the Regulatory Landscape and Functional Diversity of RNA Polymerase II CTD Phosphorylation

| PRJNA1213690 | ENA

DSIF and RNA polymerase II CTD Phosphorylation Coordinate the Recruitment of Rpd3S to Actively Transcribed Genes

Project description:Histone deacetylase Rpd3 is part of two distinct complexes: the large (Rpd3L) and small (Rpd3S) complexes. While Rpd3L targets specific promoters for gene repression, Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II, to prevent cryptic initiation within genes. Methylation of histone H3 at lysine 36 by the Set2 methyltransferase is thought to mediate the recruitment of Rpd3S. Here, we confirm by ChIP-Chip that Rpd3S binds active ORFs. Surprisingly, however, Rpd3S is not recruited to all active genes, and its recruitment is Set2-independent. However, Rpd3S complexes recruited in the absence of H3K36 methylation appear to be inactive. Finally, we present evidence implicating the yeast DSIF complex (Spt4/5) and RNA polymerase II phosphorylation by Kin28 and Ctk1 in the recruitment of Rpd3S to active genes. Taken together, our data support a model where Set2-dependent histone H3 methylation is required for the activation of Rpd3S following its recruitment to the RNA polymerase II C-terminal domain. In order to examine the genome-wide localization of RNAPII and Spt6 in Saccharomyces cerevisiae, RNAPII and Spt6 along with associated DNA sequences were immunoprecipitated using anti-8WG16 and anti-HA antibodies, respectively. The RNAPII and Spt6 chromatin immunoprecipitation was performed in duplicate from WT cells as described below. The extracted DNA was hybridized to a DNA microarray containing an average of 4 probes per kilobase across the whole yeast genome. The combined datasets are available in the supplemental files of the related publication.

2010-11-28 | E-GEOD-22636 | biostudies-arrayexpress

Expanding the CTD code: methylation of non-consensus Lysine residues marks early transcription in mammalian cells

Project description:Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and co-transcriptional processing of nascent RNA. Extensive phosphorylation of serine residues occurs at the structurally-disordered C-terminal domain (CTD) of the largest RNAPII subunit, which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe for the first time mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. Genome wide mapping of 2 novel RNAPII post-translational modifications (CTD-K7me1 and CTD-K7me2) in mouse ES cells.

2015-12-22 | E-GEOD-72876 | biostudies-arrayexpress

ENCODE: two phosphorylation states of RNAP II ChIP-chip from HeLa cells

Project description:Two phosphorylation states of RNAPII in HeLa cells Keywords: ChIP-chip Study of RNAPII binding patterns to ENCODE regions. 3 arrays using 8wg16 antibody, hypophosphoryated PolII, 3 arrays using 4H8 antibody, phosphorylated PolII CTD, and 6 input DNA arrays.

2010-06-10 | E-GEOD-2735 | biostudies-arrayexpress

RNA Polymerase II interactome in presence or absence of SCAF1 in U2OS-SCAF1-AID cells

Project description:Transcripts produced by RNA polymerase II (RNAPII) are fundamental for cellular responses to environmental changes. It is therefore no surprise that there exist multiple avenues for the regulation of this process. To explore the regulation mediated by RNAPII-interacting proteins, we used an siRNA-based screen to systematically evaluate their influence on RNA synthesis. We identified several proteins that strongly affected RNAPII activity. We evaluated one of the top hits, SCAF1, using an auxin-inducible degradation system and sequencing approaches. In agreement with our screen results, acute depletion of SCAF1 decreased RNA synthesis, and showed an increase of Serine-2 phosphorylated-RNAPII (pS2-RNAPII). We found that the accumulation of pS2-RNAPII within the gene body occurred at GC-rich regions and was indicative of stalled RNAPII complexes. The accumulation of stalled RNAPII complexes was accompanied by reduced recruitment of initiating RNAPII, explaining the observed global decrease in transcriptional output. Furthermore, upon SCAF1 depletion, RNAPII complexes showed increased association with components of the proteasomal-degradation machinery. We concluded that in cells lacking SCAF1, RNAPII undergoes a rather interrupted passage, resulting in intervention by the proteasomal-degradation machinery to clear stalled RNAPII. While cells survive the compromised transcription caused by absence of SCAF1, further inhibition of proteasomal-degradation machinery, is synthetically lethal.

2024-12-20 | PXD054675 | Pride

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).

2023-07-25 | GSE207269 | GEO

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