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Role of NuRD subunits CHD3 and CHD4 in human melanoma cells

ABSTRACT: Role of NuRD subunits CHD3 and CHD4 in human melanoma cells

PROVIDER: PRJNA556637 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9833130.fastq.gz	Fastqsanger.gz
	SRR9833121.fastq.gz	Fastqsanger.gz
	SRR9833131.fastq.gz	Fastqsanger.gz
	SRR9833122.fastq.gz	Fastqsanger.gz
	SRR9833132.fastq.gz	Fastqsanger.gz

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Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (RNA-seq)

Project description:The Nuclesome Remodelling and Deacetylation (NuRD) complex is an epigenetic regulator of gene expression comprising two mutually exclusive ATPase subunits CHD3 or CHD4. Here we show that CHD4 silencing in multiple types of cancer cells de-represses expression of the PADI1 (Protein Arginine Deiminase 1) and PADI3 enzymes that convert arginine to citrulline. Increased PADI1 and PADI3 expression enhances citrullination of three arginines of the key glycolytic regulatory enzyme PKM2 (pyruvate kinase) promoting excessive glycolysis, lowered ATP levels and slowed proliferation. PKM2 citrullination lowers its sensitivity to the allosteric inhibitors Tryptophan and Phenylalanine shifting equilibrium towards the allosteric activator Serine, thereby bypassing the normal physiological regulation of glycolysis by low Serine levels. Our results describe a novel pathway linking epigenetic regulation of PADI1 and PAD3 expression by CHD4 to glycolytic flux and the control of cancer cell growth.

2019-11-03 | GSE134849 | GEO

Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (ChIP-seq)

2019-11-03 | GSE134848 | GEO

Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (ChIP-seq)

Project description:Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (ChIP-seq)

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Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (RNA-seq)

Project description:Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (RNA-seq)

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CHD3 and CHD4 coordinate gene expression programs to maintain β-cell function and identity in vivo

Project description:To establish the role of CHD3 and CHD4 on controlling human gene expression programs in the islet, we generated pseudoislets from non-diabetic human donors that were treated with shRNA for CHD3, CHD4 or CHD3+CHD4. mRNA-Seq was performed on isolatd RNA from pseudoislets

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Evaluating and comparing the Transcriptome of (human) Hek 293 based cells, expressing either CHD3 or CHD4

Project description:Purpose: Identifying target genes of the two human chromatin remodeling enzymes CHD3 and CHD4 Methods: see below in protocols Results: Libraries were sequenced on Illumina HiSeq2000 platform resulting in 37-71 Mio 50 bp paired-end reads per sample. We identified 16 (i) and 115 (ii) distinctly regulated genes when CHD3-GFP (i) or CHD4-GFP (ii) were overexpressed. Nine genes seem to be commonly regulated by CHD3 and CHD4. We successfully validated four genes from our RNA-seq via qPCR with two new (independent from those, used for RNA-seq) biological replicates. Conclusion: CHD3 and CHD4 regulate distinct genes.

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CHD3 and CHD4 coordinate gene expression programs to maintain β-cell function and identity in vivo [RNA-seq]

Project description:To establish the role of CHD3 and CHD4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse models; control (MIP-CreERT; Chd3+/+; Chd4+/+; R26RtdTomato), Chd3Db (MIP-CreERT; Chd3f/f; Chd4+/+; R26RtdTomato) and Chd3/4Db (MIP-CreERT; Chd3f/f; Chd4f/f; R26RtdTomato)

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Project description:To establish the role of CHD3 and CHD4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse models; control (MIP-CreERT; Chd3+/+; Chd4+/+; R26RtdTomato) and Chd3/4Db (MIP-CreERT; Chd3f/f; Chd4f/f; R26RtdTomato)

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Project description:Dynamic changes of histone epigenetic modifications and chromatin structure represent an universal mechanism by which cells adapt their transcriptional response to rapidly changing environmental conditions. During neuronal development, extensive chromatin remodeling takes place allowing the transition of pluripotent cells into differentiated neurons. Here we report that the ATP-dependent chromatin remodeling complex NuRD, which couples ATP-dependent nucleosome sliding with histone deacetylase activity, is a major remodeling complex in embryonic brain and plays an instructive role during mouse neuronal development. Importantly, the ATPase subunits of NuRD complex CHD3, CHD4 and CHD5 undergo a functional switch, thereby regulating distinct aspects of neuronal differentiation and migration in a sequential and mostly non-overlapping manner. We conclude that the recruitment of NuRD complexes containing specific CHDs to gene promoters and enhancers plays an instructive role in brain development. Gene expression analysis was performed in the mouse embryonic cortex at three developmental stages: E12.5, E15.5 and E18.5 using total RNA obtained from four embryos for each time point.

2015-06-27 | E-GEOD-70298 | biostudies-arrayexpress

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