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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

CHD1 Loss Hijacks SREBP2-mediated Cholesterol Biosynthesis to Fuel SPOP-deficient Prostate Cancer and Confers Resistance to Castration

Project description:Androgen receptor (AR) is an important driver in the disease progression of castration-resistant prostate cancer (CRPC). Speckle-type BTB/POZ protein (SPOP) mutations stabilize AR and frequently co-occur with the loss of chromodomain helicase DNA-binding protein 1 (CHD1). We generated a new genetically engineered mouse model and prostate cancer cells model containing CHD1 deletion and SPOP mutation to study the underlying mechanism. We found CHD1 loss–induced cholesterol production supplies intratumoral androgen biosynthesis and retains AR transcriptional activity in SPOP-mutated prostate tumors, leading to castration resistance.

2025-02-10 | GSE272802 | GEO

Intrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks

Project description:Metazoans employ chromodomain helicase DNA-binding (CHD) enzymes to reposition nucleosomal DNA for transcription and replication. The CHD family consists of nine distinct members (CHD1-9) that possess highly conserved chromo and ATPase domains. These domains are flanked by poorly characterised N- and C-termini, which are enriched with intrinsically disordered regions (IDRs) and short aggregation-prone regions (APRs). The contribution of IDRs and APRs to CHD function has remained elusive. In this study we used affinity purification followed by mass spectrometry analysis (AP-MS) to define the protein-protein interaction (PPI) networks within the N- and C-termini of each CHD family member. The results illustrate a comprehensive map of CHD1-9-specific binding proteins that include dozens of novel interactions with transcription regulators and epigenetic factors. Using AlphaFold Multimer we examined the structural predictions of high confidence PPIs from our AP-MS screens and identified APR regions with alpha helical structures that contribute to PPIs. We further investigated a highly conserved APR within the C-terminus of the CHD4 protein and demonstrate that it contributes to the interaction of CHD4 with the nucleosome remodelling and deacetylase (NuRD) and CHD, ADNP, HP1 (ChAHP) complexes. Peptides mimicking this APR effectively disrupt CHD4 binding to both NuRD and ChAHP complexes, consequently triggering the transcriptional activation or repression of hundreds of target genes. Our results emphasise the crucial role that the N- and C-termini of CHD chromatin remodelers play in establishing protein-protein interaction (PPI) networks, which drive unique transcriptional programs.

2025-05-26 | PXD055009 | Pride

CHD1 Loss Hijacks SREBP2-mediated Cholesterol Biosynthesis to Fuel SPOP-deficient Prostate Cancer and Confers Resistance to Castration [scRNA-seq]

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Intrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks

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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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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

| PRJNA610426 | ENA

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.

2025-02-19 | GSE146232 | GEO

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