Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [ChIP-seq]

ABSTRACT: RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [ChIP-seq]

PROVIDER: PRJNA607254 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11100916.fastq.gz	Fastqsanger.gz
	SRR11100917.fastq.gz	Fastqsanger.gz
	SRR11100918.fastq.gz	Fastqsanger.gz
	SRR11100919.fastq.gz	Fastqsanger.gz
	SRR11100920.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [RNA-seq]

Project description:We show that inactivating CDK-12 or expressing a full-length CTD S2A mutant in Caenorhabditis elegans results in developmental arrest at the L1 stage,which mimicks the diapause induced when hatching occurs in the absence of food. Transcriptomic analyses indicate that when CDK-12 is inhibited, only a subset of growth-related genes is not properly expressed. These genes correspond to SL2 trans-spliced mRNAs located in position 2 and over within operons. We show that CDK-12 is required for maximal occupancy of CstF (cleavage stimulatory factor) required for SL2 trans-splicing. The addition of food to developmentally arrested worms leads to an increase of both CTD S2P and SL2 trans-splicing. We propose that CTD S2P functions as a gene-specific signaling mark ensuring the nutritional control of C. elegans development.

2020-10-20 | GSE145457 | GEO

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [ChIP-seq]

2020-10-20 | GSE145456 | GEO

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans

Project description:RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans

| PRJNA607250 | ENA

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [RNA-seq]

Project description:RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [RNA-seq]

| PRJNA607253 | ENA

RNA polymerase II CTD S2P is dispensable for embryogenesis but mediates exit from developmental diapause in C. elegans.

Project description:Serine 2 phosphorylation (S2P) within the CTD of RNA polymerase II is considered a Cdk9/Cdk12-dependent mark required for 3'-end processing. However, the relevance of CTD S2P in metazoan development is unknown. We show that cdk-12 lesions or a full-length CTD S2A substitution results in an identical phenotype in Caenorhabditis elegans Embryogenesis occurs in the complete absence of S2P, but the hatched larvae arrest development, mimicking the diapause induced when hatching occurs in the absence of food. Genome-wide analyses indicate that when CTD S2P is inhibited, only a subset of growth-related genes is not properly expressed. These genes correspond to SL2 trans-spliced mRNAs located in position 2 and over within operons. We show that CDK-12 is required for maximal occupancy of cleavage stimulatory factor necessary for SL2 trans-splicing. We propose that CTD S2P functions as a gene-specific signaling mark ensuring the nutritional control of the C. elegans developmental program.

| S-EPMC7725455 | biostudies-literature

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.

2023-06-21 | GSE210601 | GEO

RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans

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

2020-10-20 | GSE145458 | GEO

A gene-specific requirement of RNA polymerase II CTD phosphorylation on serine 2 for sexual differentiation in fission yeast

Project description:The switch from cellular proliferation to differentiation occurs to a large extent through specific programs of gene expression. In fission yeast, the master regulator of sexual differentiation, ste11, is induced by environmental conditions leading to mating and meiosis. We show that phosphorylation of serine 2 (S2P) in the C-terminal domain (CTD) of the largest subunit of the RNA polymerase II (PolII) enzyme by the Lsk1 cyclin dependent kinase has only a minor impact on global gene expression during vegetative growth but is critical for the induction of ste11 transcription during sexual differentiation. The recruitment of the Lsk1 kinase initiates in the vicinity of the transcription start site of ste11, resulting in a marked increase of S2P on the ste11 unit including an extended 5’-untranslated region (5’-UTR). This pattern contrasts with the classical gradient of S2P towards the 3’ region. In the absence of S2P, both PolII occupancy at the ste11 locus and ste11 expression are impaired. This results in sterility which is rescued by expression of the ste11 coding sequence from the adh1 promoter. Thus, the S2P polymerase plays a specific, regulatory role in cell differentiation through the induction of ste11.

2010-01-01 | GSE16498 | GEO

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

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

| PRJNA866471 | ENA

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

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