Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CTDP1 and RPB7 stabilize and license Pol II termination to reinitiation [PRO-seq]

ABSTRACT: The regulations of RNA Pol II initiation, elongation, and termination have been extensively investigated in mammalian cells, but how RNA Pol II terminates and then reinitiates a new round of transcription remains elusive. Here, we found that RPB7 loss triggers the degradation of RNA Pol II. Strikingly, RPB7 degradation combines knock out of E3 ligase Cullin 3 led to the accumulation of phosphorylated Pol II in the soluble fractions and Pol II reinitiation failure. The stability of recycled Pol II is dependent on the loop domain of RPB7 and the dephosphorylation of Pol II CTD. Termination-reinitiation recycling requires RPB7, CTD phosphatase subunit 1 (CTDP1), and stabilization of Pol II. Our study demonstrates that RPB7/CTDP1 controls the dephosphorylation and stabilization of RNA Pol II to permit RNA Pol II termination to reinitiation recycle in mammalian cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE255170 | GEO | 2025/02/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CTDP1 and RPB7 stabilize and license Pol II termination to reinitiation [Micro-C]

Project description:The regulations of RNA Pol II initiation, elongation, and termination have been extensively investigated in mammalian cells, but how RNA Pol II terminates and then reinitiates a new round of transcription remains elusive. Here, we found that RPB7 loss triggers the degradation of RNA Pol II. Strikingly, RPB7 degradation combines knock out of E3 ligase Cullin 3 led to the accumulation of phosphorylated Pol II in the soluble fractions and Pol II reinitiation failure. The stability of recycled Pol II is dependent on the loop domain of RPB7 and the dephosphorylation of Pol II CTD. Termination-reinitiation recycling requires RPB7, CTD phosphatase subunit 1 (CTDP1), and stabilization of Pol II. Our study demonstrates that RPB7/CTDP1 controls the dephosphorylation and stabilization of RNA Pol II to permit RNA Pol II termination to reinitiation recycle in mammalian cells.

2025-02-05 | GSE255169 | GEO

RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [ChAR-Seq]

Project description:The regulations of transcription process have been extensively investigated, but how RNA Pol II terminates and reinitiates a new round of transcription remains elusive. Here, we found that RPB7 loss triggers the degradation of RNA Pol II. RPB7 degradation combing knock out of E3 ligase Cullin 3 led to the accumulation of phosphorylated Pol II in the soluble fractions and Pol II reinitiation failure. The stability of recycled Pol II is dependent on the loop-region and dimerization of RPB7 and the phosphorylation state of Pol II CTD. Site-specific cancer mutations in the RPB7 loop-region caused the dysregulations of specific gene expression. Moreover, the loss of RPB7 or CTD phosphatase subunit 1 (CTDP1) result in the defects in Pol II termination-reinitiation recycle. Together, our study demonstrates that RPB7/CTDP1 controls the dephosphorylation and stabilization of RNA Pol II to permit RNA Pol II termination to reinitiation recycle in mammalian cells.

2025-02-05 | GSE223473 | GEO

RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [RNA-Seq]

2025-02-05 | GSE223472 | GEO

RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [ChIP-Seq]

2025-02-05 | GSE223474 | GEO

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.

2022-03-29 | GSE164277 | 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

The Ess1 prolyl isomerase is required for the transcription termination of small non-coding RNAs via Nrd1 pathway

Project description:Genome-wide studies have identified abundant small, non-coding RNAs including snRNAs, snoRNAs, cryptic unstable transcripts (CUTs), and upstream regulatory RNAs (uRNAs) that are transcribed by RNA polymerase II (pol II) and terminated by a Nrd1-dependent pathway. Here, we show that the prolyl isomerase, Ess1, is required for Nrd1-dependent termination of ncRNAs. Ess1 binds the carboxy terminal domain (CTD) of pol II and is thought to regulate transcription by conformational isomerization of Ser-Pro bonds within the CTD. In ess1 mutants, expression of ~10% of the genome was altered, due primarily to defects in termination of snoRNAs, CUTs, SUTs and uRNAs. Ess1 promoted dephosphorylation of Ser5 (but not Ser2) within the CTD, most likely by the Ssu72 phosphatase, and we provide evidence for a competition between Nrd1 and Pcf11 for CTD-binding that is regulated by Ess1-dependent isomerization. This is the first example of a prolyl isomerase required for interpreting the “CTD code.”

2009-10-16 | GSE17638 | GEO

Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation

Project description:The Piwi-interacting RNA (piRNA) pathway plays a crucial role in protecting animal germ cells by repressing transposons. However, the mechanism behind this RNA-mediated epigenetic regulation that leads to heterochromatin formation is not yet fully understood. Through RNA interference screens, we discovered Pcf11 and PNUTS, two conserved termination factors of RNA polymerase II (Pol II), as essential for piRNA-guided silencing. When Pcf11 is artificially tethered to a reporter, it leads to co-transcriptional repression and Pol II stalling, both of which are dependent on an alpha-helical region of Pcf11 capable of forming condensates when triggered by the C-terminal repeat domain (CTD) of Pol II. Interestingly, an intrinsically disordered region (IDR) derived from the Plant FCA can substitute for the alpha-helical region of Pcf11 in its silencing capacity and support animal development, demonstrating a causal relationship between phase separation and Pcf11’s function. Further exploration into how Pcf11 causes Pol II stalling revealed a direct interaction between Pcf11’s CTD-interaction domain (CID) and a CTR region of Spt5. The dephosphorylation of Spt5-CTR by PP1/PNUTS is essential for Pcf11’s recruitment during Pol II termination. It appears that the phosphorylated state of CTR inhibits Pcf11 condensate formation, while the phosphorylation of Pol II CTD at Threonine 4 enhances Pcf11’s ability to undergo phase separation. In conclusion, we propose a model in which Pcf11 regulates transcriptional termination by slowing down Pol II elongation, a process that is aided by phase separation with the unphosphorylated Spt5. The ability of Pcf11 to stall Pol II, utilized by the piRNA pathway to initiate heterochromatin formation, might represent a universal strategy for nascent RNA-mediated epigenetic control.

2025-01-27 | GSE261847 | 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

Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing

Project description:We have generated single-nucleotide resolution, nascent transcription profiles from HeLa cells by developing Native Elongation Transcript sequencing technology for mammalian chromatin (mNET-seq). Our extensive data sets provide a substantial resource to study mammalian nascent transcript profiles. We reveal unanticipated phosphorylation states for RNA polymerase II C-terminal domain (Pol II CTD) at both gene ends. We also observe that following 5’ splice site cleavage by the spliceosome, upstream exon transcripts are tethered to Pol II CTD phosphorylated on the serine 5 position (S5P) which is accumulated over downstream exons. We further show that depletion of termination factors substantially reduces Pol II pausing at gene ends leading to termination defects. Remarkably termination factors play an additional promoter role by restricting non-productive RNA synthesis and redistributing Pol II CTD S2P to promoters. These data demonstrate that CTD phosphorylation is more dynamic and variably distributed across mammalian transcription units than previously envisaged. To monitor nascent RNA within the mammalian Pol II complex, and its association with different CTD phosphorylation states, we employed mNET-seq methodology on HeLa cells, complemented with direct sequencing of chromatin-bound RNA (ChrRNA-seq). mNET-seq was preformed using the antibodies 8WG16, CMA602, CMA603 and CMA601, which are specific for unphosphorylated CTD, Ser2 phosphorylation, Ser5 phosphorylation and all CTD isoforms, respectively. In another experiment, to evaluate the effect of transcription termination factors in nascent RNA production by Pol II, mNET-seq and complemented with ChrRNA-seq was preformed on HeLa cells transfected with siRNA against PTBP1, CPSF73, CstF64+CstF64tau or Xrn2, and the gene profiles were compared with profiles from HeLa transfected with siRNA for Luciferase generated by the same protocol.

2015-04-23 | E-GEOD-60358 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data