Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA254837 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Regions of H3.3 binding in WT and ATRX KO mouse ES cells were identified by ChIP seq Chip-seq experiements were performed in WT and ATRX KO E14 mouse ES cells
2015-04-16 | E-GEOD-59270 | biostudies-arrayexpress
Project description:Regions of H3.3 binding in WT and ATRX KO mouse ES cells were identified by ChIP seq
2015-04-16 | GSE59270 | GEO
Project description:Analysis of gene expression in WT and ATRX KO Cast x 129 Mouse ES cells Paired end RNA-seq analysis of PolyA selected RNA and PolyA depeleted RNA from in both wildtype nd ATRX knocked out Castx129 Mouse ES Cells
2015-04-16 | E-GEOD-59269 | biostudies-arrayexpress
Project description:The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem (ES) cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence, and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres, and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells. Crosslinking ChIP-seq: Examination of 1 histone variant (H3.3), 2 histone modifications, and Serine-5 phosphorylated RNA polymerase in 2 different cell types (H3.3-HA ES samples 1-4, and H3.3-HA NPC samples 7-10). Examination of 1 histone variant (H3.2), and one histone modification (H3K36me3) in 2 different cell types (H3.2-HA ES samples 5-6, and H3.2-HA NPC samples 11-12). Examination of 1 histone variant (H3.3), input control, and one histone modification (H3K36me3) in one cell type (H3.3-HA hybrid ES, samples 13-15). Examination of 1 histone variant (H3.1S31), input control, and one histone modification (H3K36me3) in one cell type (H3.1S31-HA hybrid ES, samples 16-18). Native ChIP-seq: Examination of 1 histone variant (H3.3), input control, and one histone modification (H3K4me3) in one cell type (H3.3-HA ES, samples 19-21). Examination of 1 histone variant (H3.2), input control, and two histone modifications (H3K4me3 and H3K27me3) in one cell type (H3.2-HA ES, samples 22-25). Examination of 1 histone variant (H3.3), input control, and two histone modifications (H3K4me1 and H3K36me3) in one cell type (H3.3-EYFP ES, samples 26-29). Examination of 1 histone variant (H3.3), input control, and two histone modifications (H3K4me1 and H3K36me3) in one cell type (Hira -/- H3.3-EYFP ES, samples 30-33). Examination of 1 histone variant (H3.3) and input control in one cell type (Atrxflox H3.3-EYFP ES, samples 34-37). Examination of HA antibody background in one cell type (wild-type ES, sample 38).
2010-03-04 | E-GEOD-16893 | biostudies-arrayexpress
Project description:Analysis of gene expression in WT and ATRX KO Cast x 129 Mouse ES cells
2015-04-16 | GSE59269 | GEO
Project description:H3.3 S31 phosphorylation ChIP-seq in mitotic WT mouse ES cells
| PRJNA753057 | ENA
Project description:Transcriptome analysis of WT and ATRX KO Cast x 129 mouse ES cells
| PRJNA254838 | ENA
Project description:Endogenous retroviruses (ERVs) comprise a significant portion of mammalian genomes. Although specific ERV loci feature regulatory roles for host gene expression, most ERV integrations are transcriptionally repressed by Setdb1 mediated H3K9me3 and DNA methylation. However, the protein network which regulates the deposition of these chromatin modifications is still incompletely understood. Here, we performed a genome-wide sgRNA screen for genes involved in ERV silencing and identified the GHKL ATPase protein Morc3 as a top-scoring hit. Morc3 knock-out cells display de-repression, reduced H3K9me3, and increased chromatin accessibility of distinct ERV families. We found that the Morc3 ATPase cycle and Morc3 SUMOylation are important for ERV chromatin regulation. Proteomic analysis revealed that Morc3 mutant proteins fail to interact with the histone H3.3 chaperone Daxx. This interaction depends on Morc3 SUMOylation and Daxx SUMO binding. Notably, in Morc3 ko cells, we observed strongly reduced histone H3.3 on Morc3 binding sites. Thus, our data demonstrate Morc3 as a critical regulator of Daxx-mediated histone H3.3 incorporation to ERV regions. This dataset comprises several experiments addressing different questions: 1. ChIP-MS experiment to determine the protein interaction context of Morc3 using a Morc3-3xFLAG knock-in ES cell line compared to wild type ES cells (Experiment 20200408). 2. ChIP-MS experiments to investigate changes in the protein interaction context of the Morc3 mutant rescue cell lines. Comparison of Morc3 knock-out cell lines with re-expression of Morc3-CW-3xFLAG mutant (Ref. #3111), Morc3-ATP-binding-3xFLAG and Morc3-SUMOylation-3xFLAG mutants (Ref. #3635), and Morc3-deltaN-3xFLAG mutant (Ref. #5174) compared to wt Morc3-3XFLAG rescue. 3. ChIP-MS experiment to determine if the interaction between Morc3 and Daxx is mediated through this C-terminal SIM, comparing Daxx knock-out cell lines with re-expression of wild type 3xFLAG-Daxx protein or 3xFLAG-Daxx ∆SIM, which lacks the C-terminal SIM domain. (Ref. #3301)
2021-11-03 | PXD027368 | Pride
Project description:ATRX is an X-linked gene of the SWI/SNF family whose role in vivo is currently unknown. Mutations in ATRX cause syndromal mental retardation. ATRX binds to tandem repeat (TR) sequences both in heterochromatin (e.g. telomeres) and euchromatin. Genes associated with these TRs can be dysregulated when ATRX is mutated and the degree to which their expression changes is determined by the size of the TR, producing skewed allelic expression. This explains the nature of the affected genes, the variable phenotypes seen with identical ATRX mutations and also illustrates a new mechanism underlying variable penetrance. Many of the TRs in ATRX targets are G-rich and predicted to form non-B DNA structures (including G quadruplex) in vivo. We have shown that ATRX binds G quadruplex structures in vitro suggesting a mechanism by which ATRX may play a role in various nuclear processes and how this is perturbed when ATRX is mutated. 4 Human Erythroblast, 1 HEP3B and 1 Fibroblast ChIP-ChIP Sample For ChIP-Seq: one human erythroblasts, one mouse ES, one human erythroblast reference Sample, and one mouse ES input reference Sample.
2010-11-02 | E-GEOD-22162 | biostudies-arrayexpress