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Gene expression profiling on heads of Drosophila chromodomain helicase DNA binding protein 1 (CHD1) deletion mutants

ABSTRACT: Gene expression profiling on heads of Drosophila chromodomain helicase DNA binding protein 1 (CHD1) deletion mutants

PROVIDER: PRJNA610298 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11237854.fastq.gz	Fastqsanger.gz
	SRR11237855.fastq.gz	Fastqsanger.gz
	SRR11237856.fastq.gz	Fastqsanger.gz
	SRR11237857.fastq.gz	Fastqsanger.gz
	SRR11237858.fastq.gz	Fastqsanger.gz

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Gene expression profiling on heads of Drosophila chromodomain helicase DNA binding protein 1 (CHD1) deletion mutants

Project description:CHD1 is a conserved ATP-dependent chromatin remodeling factor with roles in transcriptional regulation and chromatin assembly. Here we show that deletion of Chd1 causes multiple behavioral and metabolic defects. In particular, it diminishes food-intake and results in shortened lifespan of mutant flies. These phenotypes can be rescued by brain-specific expression of Chd1 via the elav promoter. Consistently, neuron-specific expression of Chd1 rescues the wide-spread transcriptional dysregulation observed in the absence of CHD1.

2021-12-07 | GSE146392 | GEO

CHD1_RIME - CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis

Project description:Crosslinked chromatin bound protein complexes were immunopurified, digested, and analyzed by mass spectrometry to identify and quantify proteins associate with the chromodomain helicase (Chd1).

2019-08-13 | PXD010468 | Pride

The Chromatin Remodeler Chromodomain Helicase DNA Binding Protein 2 Promotes Colorectal Cancer Progression

Project description:The Chromatin Remodeler Chromodomain Helicase DNA Binding Protein 2 Promotes Colorectal Cancer Progression

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Chromodomain Helicase DNA-binding 4 (CHD4) is required for B cell identity and lineage progression

Project description:B cell specification and identity are controlled by transcription factors and cytokine receptors that drive the expression of stage-specific transcriptomes during lineage progression. A key feature of these mechanisms is the repression of inappropriate transcription. Here, we utilized RNA-seq to demonstrate that chromodomain helicase DNA-binding protein 4 (CHD4), an ATPase/helicase subunit of Mi-2/NuRD chromatin remodeling complexes, is essential for B cell identity. In mice that lack CHD4 selectively in the B lineage, defects include developmental arrest at the early pro-B cell stage. While many pro-B-specific genes are expressed in the mutant cells, transcripts that are normally restricted to other tissues including pancreas and bone are expressed out of context. Moreover, CHD4-deficient pro-B cells do not proliferate in response to IL-7, exhibit greatly decreased utilization of distal VH segments and accumulate DNA damage. Together, our data confirm the importance of CHD4 and NuRD complexes for the generation of functional B cells.

2019-05-22 | GSE84806 | GEO

The Chromatin Remodeler Chromodomain Helicase DNA Binding Protein 2 Promotes Colorectal Cancer Progression

Project description:Integrative analysis of colorectal cancer (CRC) whole genomes and matched transcriptomes revealed that somatic promoter mutations are associated with increased Chromodomain helicase DNA-binding protein 2 (CHD2) levels. In both primary and metastatic CRC patients, elevated CHD2 levels are associated with worse prognosis and overall survival. We find that CHD2 increases promoter-transcription start site-chromatin accessibility and transcriptional upregulation of multiple oncogenes. In vitro, elevated CHD2 promoted CRC cell proliferation, migration and growth. In orthotopic xenografts, CHD2 promoted higher tumor burden and abdominal metastases, most prominently to the liver. FTD/TPI is an FDA approved chemotherapy for advanced chemo-refractory CRC. In orthotopic CRC models, FTD/TPI was highly effective in reducing metastases and prolonging survival for CHD2 high expressing CRCs. Thus, high CHD2 expression may be a potential CRC chemopredictive biomarker for FTD/TPI. Overall, these results provide new insights into the role of non-coding mutations and CHD2 levels to promote CRC growth and metastasis.

2021-02-12 | GSE146398 | GEO

Deletion of nucleoporin Seh1 impaired neurogenesis through transcriptional regulation (ChIP-Seq)

Project description:Nucleoporin Seh1 and chromodomain helicase DNA binding protein 4 have been involved in gene regulation. To dissect direct regulated genes, we performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for nucleoporin Seh1 or chromodomain helicase DNA binding protein 4 in neural stem cells.

2023-05-29 | GSE233613 | GEO

heads only

Project description:heads only

| PRJNA87985 | ENA

Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA.

Project description:Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

| S-EPMC3234930 | biostudies-literature

Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains

Project description:Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains.

2012-07-25 | GSE32043 | GEO

Microarray of CHD1 Knockdown in PC3 cells and CHD1 knockout in LNCaP cells

Project description:We used microarrays to study the global gene expression and identified differentially expressed genes in CHD1 knockdown PC-3 cells and CHD1 KO LNCaP cells, aiming to identify genes and pathways that are regulated by CHD1

2017-02-10 | GSE84970 | GEO

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