Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-Seq mapping of H2AK5ac, H2AK9ac, DNTTIP1, MIDEAS, and LIG4 at AsiSI-induced DNA double-strand breaks in control or MiDAC-deficient cells

ABSTRACT: To test whether MiDAC-promoted H2AK5/K9 deacetylation is implicated in DSB response, we took advantage of an improved DSB-induced via AsiSI (AiDIvA) system, in which the endonuclease restriction enzyme AsiSI is fused to the estrogen receptor (ER) hormone-binding domain and its nuclear expression in HeLa cells is controlled by doxycycline and 4-hydroxy tamoxifen (4-OHT). The precise distribution of gH2AX, H2AK5ac, H2AK9ac, FLAG-DNTTIP1, FLAG-MIDEAS, and LIG4 at AsiSI-induced DNA double-strand breaks was determined by chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq). ChIP signals from ER-AsiSI-expressing AiDIvA cells (DSB group) were normalized to ER-expressing control cells (Ctrl group).

ORGANISM(S): Homo sapiens

PROVIDER: GSE235845 | GEO | 2024/02/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization

Project description:Purpose: Evaluate how ARP2/3-coupled DSB mobility affects chromatin organization (Hi-C) and translocation frequency (HTGTS) in mouse embryonic fibroblasts (MEFs) harboring an inducible AsiSI restriction enzyme. MEF Hi-C Methods: Damaged samples were treated with 3 ug/mL doxycycline for 24 hours. For the last 6 hours of doxycycline treatment, 1 ug/mL 4-OHT was used to induce AsiSI translocation to the nucleus, triggering DSBs. Cells were co-treated with DMSO, 100 μM CK-666, or 10 μM NU7441. For DNA-PKcs inhibitor experiments, cells were pretreated with 10 μM NU7441 for 1 hour prior to induction of damage with 4OHT. 2 biological replicates were performed for each experimental condition. MEF HTGTS Methods: WT MEFs and AsiSI MEFs were treated as above. Following 6 hours treatment with dox and 4OHT, cells were lysed. For WASP inhibition, cells were treated with 3 μM wiskostatin following induction of damage. For flag-actin experiments, AsiSI-MEF cells were transfected with Flag–actinR62D–NLS 24 hours prior to induction of AsiSI expression. For cas9 experiments, WT MEF cells were transfected with sgRNA targeting Chr2 48 hours prior to cell lysis.

2022-11-14 | GSE183059 | GEO

Role of Polycomb group proteins in the DNA damage response – a reassessment

Project description:We have investigated whether components of Polycomb repressive complex 1 (PRC1) are recruited to double-strand breaks (DSBs) generated by inducible expression of the AsiSI restriction enzyme in normal human fibroblasts. Using chromatin immunoprecipitation and deep sequencing (ChIP-seq), which detects PRC1 proteins at common sites throughout the genome, we did not find evidence for recruitment of PRC1 components to AsiSI-induced DSBs. In contrast, the S2056 phosphorylated form of DNA-PKcs and other DNA repair proteins were detected at a subset of AsiSI sites that are predominantly at the 5’ ends of transcriptionally active genes. Our data question the idea that PcG protein recruitment provides a link between DSB repairs and transcriptional repression. Single chromatin preparations from treated and untreated cells (+/- OHT), immunoprecipitated with two antibodies (pDNA-PKcs and MEL18) were sequenced as technical replicates, along with the corresponding input DNAs

2014-07-06 | E-GEOD-55605 | biostudies-arrayexpress

ChIP-Seq mapping of H2AK5ac, H2AK9ac, DNTTIP1, MIDEAS, and LIG4 at AsiSI-induced DNA double-strand breaks in control or MiDAC-deficient cells

Project description:ChIP-Seq mapping of H2AK5ac, H2AK9ac, DNTTIP1, MIDEAS, and LIG4 at AsiSI-induced DNA double-strand breaks in control or MiDAC-deficient cells

| PRJNA987699 | ENA

The interdependency between MiDAC complex and MLL3/4 complexes

Project description:Enhancers play a pivotal role in gene transcriptional regulation in response to developmental cues. Active enhancers are marked by H3K4me1/2 and H3K27ac, while poised enhancers are marked by H3K27me3 instead of H3K27ac in addition to H3K4me1/2. How these histone modifications and/or other histone modification(s) at enhancers are regulated remains not fully understood. Through immunoprecipitation followed by mass spectrometry of UTX, a specific subunit of the enhancer associated COMPASS complex: MLL3/4, we identified DNTTIP1 and ELMSAN1, which are scaffolds of the mitotic deacetylase complex (MiDAC), as new UTX interactors. Our biochemistry data shows that UTX-ELMSAN1 is the interface between MiDAC and MLL3/4 complexes. The loss of MiDAC causes genome wide increase of H4K20ac, suggesting H4K20ac is a MiDAC substrate in vivo. H4K20ac is genome-wide co-localized with H3K4me1/2, H3K27ac, UTX, and MLL4, suggesting it is located at active enhancers. Genome-wide increased occupancy of UTX and MLL4 is observed at Dnttip1 knockout mES cells, which means under normal conditions MiDAC may repress MLL3/4-UTX’s genomic localization. However, we observe an increase of H3K4me2 but not H3K4me1 at those UTX & MLL4 increased loci. In MLL3/4 double knockout mES cells, Dnttip1 is reduced genome-wide, which however does not lead to a genome-wide increase of H4K20ac, but a genome-wide loss of it. At either H4K20ac or Dnttip1 reduction loci, we observe an increase of H3K27me3, suggesting the formation of repressed chromatin state which may suppress the increase of H4K20ac at Dnttip1 reduced loci. Our study for the first time reveals the functional intersection between MiDAC and MLL3/4 complexes.

2022-06-27 | GSE190323 | GEO

GATAD2B containing NuRD complex drives R-loop dependent chromatin boundary formation at double strand breaks

Project description:To understand how components of NuRD could be recruited to DNA double-stranded break sites, we generate site-specific DNA double strand breaks through an inducible endonuclease AsiSI-ER system by adding 4-OHT, we applied antibodies against GATAD2B and HDAC1, both of which are components of NuRD complex, to pero ChIP in either DMSO or 4OHT treatment condition.

2024-04-17 | GSE230710 | GEO

The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression to control neurite outgrowth [RNA-Seq]

Project description:Cell type diversity during neuro-ectodermal (NE) differentiation is achieved through selective activation and silencing of neurodevelopmental genes. Here, we show a key role for the histone deacetylase complex MiDAC during neuronal differentiation of mouse embryonic stem cells (mESCs) into NE. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC mediates the removal of H4K20ac on the promoters and enhancers of pro-neural genes such as the axon guidance ligands Slit3 and Ntn1 while in parallel reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis thereby upregulating and inhibiting gene expression, respectively. Furthermore, neurite outgrowth defects in MiDAC KO neurons can be rescued by restoring Slit3/Robo3-Ntn1/Unc5b signaling. Taken together, our work suggests a crucial role for MiDAC in regulating the secretome of the Slit3/Robo3-Ntn1/Unc5b signaling axes to ensure the proper integrity of neurite development.

2020-04-08 | GSE131060 | GEO

The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression to control neurite outgrowth [ChIP-Seq]

2020-04-08 | GSE131061 | GEO

iMUT-seq analysis of over 20 different DSB repair siRNA mediated knockdowns or small molecule inhibitors

Project description:iMUT-seq profiles double-strand break (DSB) induced mutations at extremely high sensitive with single nucleotide resolution, allowing for the quantification of all mutation types, including chromosomal rearrangements, around endogenous DSBs. AID-DIvA cells are treated with or without 4-hydroxytamoxifen to induce DSBs, then with IAA to induce degradation of the DSB inducing AsiSI enzyme and are then incubated to allow the breaks to be repaired. The DSB loci are then PCR amplified from the genomic DNA and subjected to NGS to provide high depth mutation profiling. All samples are either untreated (m/0) or treated (p/4)with OHT and have three independent biological replicates, with the exception of ATRi which has 2 replicates and controlsi which has 6 replicates. This is because the siRNA were divided into two batches to create replicates 1-3 and 4-6 and each batch contained a controlsi sample for reference causing it to be in all 6 replicates.

2022-11-25 | E-MTAB-11259 | biostudies-arrayexpress

DRIP-seq files for: DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci

Project description:Determining the role of DDX17 in the formation of DNA:RNA-hybrids around active DNA double-strand breaks (DSBs) using DRIP-seq in the damaged induced via AsiSI (DIvA) cell system that induced DSBs at known genomic loci in response to hydroxytamoxifen (OHT) treatment via and AsiSI enzyme fused to an oestrogen receptor. Sequencing was done using either control or DDX17 siRNA, and mock or 4 hours 300nM OHT treatment. Paired-end 150 cycles was completed on an Illumina NextSeq 500 and library prep was completed using the NEB NEBNext Ultra II library prep kit.

2022-11-08 | E-MTAB-10814 | biostudies-arrayexpress

Genome-wide DNA damage response following ionizing radiation

Project description:H2AX phosphorylation at Ser139 (gH2AX) is an early key event of the DNA damage response (DDR) following DNA double strand breaks (DSB) induction. Although gH2AX distribution has been extensively used as a damage marker, genome-wide investigation of the subsequent DNA repair has been poorly addressed. Here we present ChIP-Seq-based distributions of Histone H3, H2AX and gH2AX under physiological conditions in HeLa cells. Additionally the same histones were studied after a single exposure to 10 Gy X-ray at 0.5, 3 and 24 hours post irradiation

2017-04-17 | GSE60526 | GEO

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