Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mus musculus

ABSTRACT: Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content [ChIP-Seq]

PROVIDER: PRJNA391576 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5749540.fastq.gz	Fastqsanger.gz
	SRR5749550.fastq.gz	Fastqsanger.gz
	SRR5749560.fastq.gz	Fastqsanger.gz
	SRR5749570.fastq.gz	Fastqsanger.gz
	SRR5749541.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 46

Similar Datasets

Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content

Project description:Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content

| PRJNA391931 | ENA

Mus musculus

Project description:Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content [RNA-Seq]

| PRJNA391579 | ENA

High Mobility Group protein mediated transcription requires DNA damage marker Î³-H2AX

Project description:The eukaryotic genome is organized into chromatin, which constitutes the physiological template for DNA-dependent processes including replication, recombination, repair and transcription. Chromatin mediated transcription regulation involves histone modifications, chromatin remodeling and DNA methylation. However, the precise biological function of non-histone chromatin-associated proteins is still unclear. The high mobility group proteins are the most abundant non-histone chromatin-associated proteins. Here we combined proteomic, ChIP-seq and transcriptome data to decipher the mechanism of transcriptional regulation mediated by the high mobility group AT-hook protein 2 (HMGA2). We showed that HMGA2-induced transcription requires H2AX phosphorylation at S139 (H2AXS139ph; Î³-H2AX), mediated by the kinase ataxia telangiectasia mutated (ATM). Furthermore, we demonstrated the relevance of this mechanism within the biological context of TGFB1-signaling. Our results link H2AXS139ph, a marker for DNA damage, to transcription, which is a new function for this histone modification. The interplay between HMGA2, ATM and H2AX is a novel mechanism of transcription initiation. Chip-seq data of HMGA2, H2AXS139ph and ATM obtained from Mouse embryonic Fibroblast cells in wt and Ko of Hmga2

2015-11-04 | E-GEOD-63861 | biostudies-arrayexpress

High Mobility Group protein mediated transcription requires DNA damage marker γ-H2AX

Project description:The eukaryotic genome is organized into chromatin, which constitutes the physiological template for DNA-dependent processes including replication, recombination, repair and transcription. Chromatin mediated transcription regulation involves histone modifications, chromatin remodeling and DNA methylation. However, the precise biological function of non-histone chromatin-associated proteins is still unclear. The high mobility group proteins are the most abundant non-histone chromatin-associated proteins. Here we combined proteomic, ChIP-seq and transcriptome data to decipher the mechanism of transcriptional regulation mediated by the high mobility group AT-hook protein 2 (HMGA2). We showed that HMGA2-induced transcription requires H2AX phosphorylation at S139 (H2AXS139ph; γ-H2AX), mediated by the kinase ataxia telangiectasia mutated (ATM). Furthermore, we demonstrated the relevance of this mechanism within the biological context of TGFB1-signaling. Our results link H2AXS139ph, a marker for DNA damage, to transcription, which is a new function for this histone modification. The interplay between HMGA2, ATM and H2AX is a novel mechanism of transcription initiation.

2015-11-04 | GSE63861 | GEO

Expression profiles in HMGN1-overexpressed neural precursor cells

Project description:Neural precursor cells (NPCs) are multipotent cells that can generate neurons, astrocytes, and oligodendrocytes in the mammalian central nervous system. Although high mobility group nucleosomal binding domain 1 (HMGN1) was highly expressed in NPCs, its functions in neural development are not fully understood. We performed microarray analysis to examine changes in gene expression between control and HMGN1-overexpressed NPCs.

2014-09-01 | GSE57534 | GEO

Hmga2 is required for canonical WNT signaling during lung development

Project description:The high-mobility-group (HMG) proteins are the most abundant non-histone chromatin-associated proteins. Here we deciphered the role of the high mobility group AT-hook protein 2 (HMGA2) during lung development by analyzing the lung of Hmga2 deficient mice (Hmga2-/-).We found that Hmga2 is expressed in the mouse embryonic lung at the distal airways. Analysis of Hmga2-/- mice showed that Hmga2 is required for proper cell proliferation and distal epithelium differentiation during embryonic lung development. Hmga2 knockout (KO) led to enhanced canonical WNT signaling due to an increased expression of secreted WNT glycoproteins Wnt2b, Wnt7b and Wnt11 as well as a reduction of the WNT signaling antagonizing proteins GATA6 (GATA binding protein 6) and FZD2 (frizzled homolog 2). Comparison of Hmga2-/- with Hmga2+/+ mice by Affymetrix microarray-based expression analysis of embryonic lung revealed an increased expression of genes whose products participate in cell cycle and canonical Wnt signaling. Affymetrix microarray transcriptome analysis of Hmga2-/- and Hmga2+/+ embryonic lung (E18.5) was performed and analyzed

2014-03-07 | E-GEOD-55340 | biostudies-arrayexpress

Transcriptome analysis upon PHF14 and HMG20A knockdown in MDA-MB-231 cells

Project description:High mobility group proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. We have shown that the high mobility group protein HMG20A copurifies with the histone reader PHF14. To understand the common functions of HMG20A and PHF14 proteins in regulating the transcriptome, we have performed RNA-Seq expression analysis following depletion of each protein in the triple-negative breast cancer cell line MDA-MB-231. Results indicate that genes regulated by PHF14 largely overlap with those regulated by HMG20A.

2022-09-05 | GSE193476 | GEO

Expression profiles in response to HMGA overexpression in late-stage neural precursor cells

Project description:Neural precursor cells (NPCs) in the mammalian neocortex generate various neuronal and glial cell types in a developmental stage-dependent manner. Most neocortical NPCs lose their neurogenic potential after birth. We have previously shown that high mobility group A (HMGA) proteins confer the neurogenic potential on early-stage NPCs during the midgestation period, although the underlying mechanisms are not fully understood. Here we performed microarray analysis and compared expression profiles between control and HMGA2-overexpressed NPCs.

2013-02-01 | GSE41882 | GEO

Hmga2 is required for canonical WNT signaling during lung development

2014-03-07 | GSE55340 | GEO

Mammalian Bcnt/Cfdp1, a potential epigenetic factor characterized by an acidic stretch in the disordered N-terminal and S250 phosphorylation in the conserved C-terminal regions

Project description:The function of mammalian Bcnt protein is poorly understood yet, though Bcnt homologs (yeast Swc5 and Dorsophila Yeti) play crucial roles in chromatin remodeling organization. In this study, we found that mammalian Bcnt protein shows unusual mobility on SDS-PAGE and is acetylated in vitro by CREB-binding protein. Therefore, we analyzed Bcnt protein by LC-MSMS to characterize the protein structure containing post-translational modifications (phosphorylation and acetylation) which may be the cause of this unusual mobility.

2017-03-29 | MSV000080755 | MassIVE

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