Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hda1C restricts burst frequency to limit divergent non-coding transcription

ABSTRACT: Hda1C restricts burst frequency to limit divergent non-coding transcription

PROVIDER: PRJNA704821 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13782634_1.fastq.gz	Fastqsanger.gz
	SRR13782634_2.fastq.gz	Fastqsanger.gz
	SRR13782635_1.fastq.gz	Fastqsanger.gz
	SRR13782635_2.fastq.gz	Fastqsanger.gz
	SRR13782636_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Hda1C restricts burst frequency to limit divergent non-coding transcription

Project description:We used Native Elongation Transcript sequencing (NET-seq) to investigate the genome-wide effect of the Hda1 histone deacetylase complex (Hda1C) on the repression of divergent non-coding (DNC) transcription at bidirectional promoters in yeast S.cerevisiae.

2021-08-02 | GSE167499 | GEO

The pause-initiation limit restricts transcription activation in human cells

Project description:Eukaryotic gene transcription is often controlled at the level of RNA polymerase II (Pol II) pausing in the promoter-proximal region. Pausing Pol II limits the frequency of transcription initiation (‘pause-initiation limit’), predicting that the pause duration must be decreased for transcriptional activation. To test this prediction, we conducted a genome-wide kinetic analysis of the heat shock response in human cells. We show that the pause-initiation limit restricts transcriptional activation at most genes. Gene activation generally requires the activity of the P-TEFb kinase CDK9, which decreases the duration of Pol II pausing and thereby enables an increase in the productive initiation frequency. The transcription of enhancer elements is generally not pause-limited and can be activated without CDK9 activity. Our results define the kinetics of Pol II transcriptional regulation in human cells at all gene classes during a natural transcription response.

2019-07-10 | GSE123980 | GEO

The pause-initiation limit restricts transcription activation in human cells

Project description:The pause-initiation limit restricts transcription activation in human cells

| PRJNA510428 | ENA

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency

Project description:PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency

| PRJNA668780 | ENA

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [RNA-seq]

Project description:The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The interrelatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population, and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control.

2021-07-21 | GSE159399 | GEO

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [ChIP-seq]

2021-07-21 | GSE159398 | GEO

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [ChIP-seq]

Project description:PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [ChIP-seq]

| PRJNA668782 | ENA

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [RNA-seq]

Project description:PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [RNA-seq]

| PRJNA668783 | ENA

WRKY6 Transcription Factor Restricts Arsenate Uptake and Transposon Activation in Arabidopsis

Project description:Stress constantly challenges plant adaptation to the environment. Of all stress types, arsenic was a major threat during the early evolution of plants. The most prevalent chemical form of arsenic is arsenate, whose similarity to phosphate renders it easily incorporated into cells via the phosphate transporters. Here we found that arsenate stress provokes a notable transposon burst in plants, in coordination with arsenate/phosphate transporter repression, which immediately restricts arsenate uptake. This repression was accompanied by delocalization of the phosphate transporter from the plasma membrane. When arsenate was removed, the system rapidly restored transcriptional expression and membrane localization of the transporter. We identify WRKY6 as an arsenate-responsive transcription factor that mediates arsenate/phosphate transporter gene expression and restricts arsenate-induced transposon activation. Plants therefore have a dual WRKY-dependent signaling mechanism that modulates arsenate uptake and transposon expression, providing a coordinated strategy for arsenate tolerance and transposon gene silencing. Three biological replicates were performed for each sample type. Single channel hybridizations were carried-out using either Affymetrix ATH1 platform or Nimblegen Gene Expression 12x135K platform (Arabidopsis thaliana).

2014-04-25 | E-GEOD-49037 | biostudies-arrayexpress

Genomic encoding of transcriptional burst kinetics

Project description:We sequenced allele-resolution single-cell transcriptomes from mouse primary fibroblasts and embryonic stem cells with the overall aim to infer transcriptional kinetics for each gene and allele. Inferred transcriptional burst kinetics revealed the genomic encoding of transcriptional burst frequencies and sizes within the genome. Core promoter elements were found to specify burst sizes, whereas burst frequencies were regulated by enhancers. In particular burst frequencies were found to account for cell-type differences in gene expression levels and were also mostly correlating with absolute expression levels in cells. Importantly, the patterns identified were not detectable at the level of mean expression demonstrating the need to investigate transcriptional dynamics at the level of burst kinetics.

2018-11-30 | E-MTAB-7098 | 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