CHD3

chromodomain helicase DNA binding protein 3 | Mi-2a, Mi2-ALPHA, ZFH

This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

Member of: DE-5 DE-5.10 Developmental clusters: GC6

Biological processes 47 terms

ATP binding (GO:0005524)ATP hydrolysis activity (GO:0016887)ATP hydrolysis activity (GO:0016887)ATP hydrolysis activity (GO:0016887)ATP-dependent chromatin remodeler activity (GO:0140658)ATP-dependent chromatin remodeler activity (GO:0140658)DNA binding (GO:0003677)DNA binding (GO:0003677)DNA binding (GO:0003677)NuRD complex (GO:0016581)NuRD complex (GO:0016581)NuRD complex (GO:0016581)NuRD complex (GO:0016581)PML body (GO:0016605)PML body (GO:0016605)RNA binding (GO:0003723)centrosome (GO:0005813)centrosome (GO:0005813)centrosome cycle (GO:0007098)chromatin (GO:0000785)chromatin binding (GO:0003682)chromatin remodeling (GO:0006338)chromatin remodeling (GO:0006338)chromatin remodeling (GO:0006338)chromatin remodeling (GO:0006338)cytoplasm (GO:0005737)helicase activity (GO:0004386)histone binding (GO:0042393)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of transcription by RNA polymerase II (GO:0000122)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of cell fate specification (GO:0042659)regulation of stem cell differentiation (GO:2000736)spindle organization (GO:0007051)transcription cis-regulatory region binding (GO:0000976)zinc ion binding (GO:0008270)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating CHD3 0 TFs

Transcription factors with Perturb-seq knockdown data for CHD3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = CHD3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to CHD3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CHD3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr17:7,588,871–7,590,534	294.6 kb	Distal (>10kb) Multiome	319
chr17:7,614,065–7,615,780	269.7 kb	Distal (>10kb) Multiome	708
chr17:7,627,090–7,628,247	257.0 kb	Distal (>10kb) Multiome	712
chr17:7,650,010–7,652,127	234.0 kb	Distal (>10kb) Multiome	467
chr17:7,685,876–7,686,907	198.5 kb	Distal (>10kb) Multiome	765
chr17:7,687,214–7,687,777	197.3 kb	Distal (>10kb) Multiome	710
chr17:7,687,867–7,688,863	196.5 kb	Distal (>10kb) Multiome	700
chr17:7,703,383–7,703,975	181.1 kb	Distal (>10kb) Multiome	141
chr17:7,704,799–7,705,590	179.7 kb	Distal (>10kb) Multiome	325
chr17:7,716,832–7,717,983	167.4 kb	Distal (>10kb) Multiome	759
chr17:7,833,417–7,837,960	49.2 kb	Distal (>10kb) Multiome	1160
chr17:7,841,438–7,843,228	42.6 kb	Distal (>10kb) Multiome	861
chr17:7,843,355–7,844,130	41.2 kb	Distal (>10kb) Multiome	614
chr17:7,844,349–7,845,186	39.9 kb	Distal (>10kb) Multiome	617
chr17:7,851,538–7,852,239	32.9 kb	Distal (>10kb) Multiome	531
chr17:7,856,600–7,858,747	27.3 kb	Distal (>10kb) Multiome	942
chr17:7,885,205–7,885,734	549 bp	At TSS Multiome	371
chr17:7,885,869–7,886,298	1.1 kb	Proximal (<10kb)	476
chr17:7,887,616–7,888,198	3.0 kb	Proximal (<10kb) Multiome	581
chr17:7,915,430–7,916,499	31.1 kb	Distal (>10kb) Multiome	869
chr17:7,922,863–7,923,421	38.2 kb	Distal (>10kb) Multiome	205
chr17:7,929,559–7,930,172	45.0 kb	Distal (>10kb) Multiome	106
chr17:7,931,533–7,932,876	47.3 kb	Distal (>10kb) Multiome	767
chr17:7,971,685–7,972,375	87.1 kb	Distal (>10kb) Multiome	45
chr17:7,989,908–7,990,676	105.5 kb	Distal (>10kb) Multiome HiCAR	652
chr17:8,015,966–8,016,968	131.2 kb	Distal (>10kb) Multiome HiCAR	339
chr17:8,068,609–8,069,844	184.0 kb	Distal (>10kb) Multiome	100
chr17:8,079,261–8,080,640	194.7 kb	Distal (>10kb) Multiome	613
chr17:8,109,567–8,110,530	225.5 kb	Distal (>10kb) Multiome	360
chr17:8,117,780–8,119,396	234.2 kb	Distal (>10kb) Multiome	684
chr17:8,119,590–8,122,560	235.8 kb	Distal (>10kb) Multiome	968
chr17:8,123,407–8,124,386	239.3 kb	Distal (>10kb) Multiome	296
chr17:8,125,308–8,126,995	240.9 kb	Distal (>10kb) Multiome	724
chr17:8,138,425–8,139,804	254.2 kb	Distal (>10kb) Multiome	981
chr17:8,151,026–8,151,640	266.5 kb	Distal (>10kb) Multiome	435
chr17:8,151,914–8,152,786	267.7 kb	Distal (>10kb) Multiome	633
chr17:8,153,878–8,154,864	269.6 kb	Distal (>10kb) Multiome	644
chr17:8,155,928–8,157,418	271.8 kb	Distal (>10kb) Multiome	789
chr17:8,162,377–8,163,907	278.3 kb	Distal (>10kb) Multiome	637
chr17:8,172,460–8,174,346	288.7 kb	Distal (>10kb) Multiome	1196
chr17:8,175,900–8,176,943	291.6 kb	Distal (>10kb) Multiome	601
chr17:8,185,937–8,188,084	302.9 kb	Distal (>10kb) Multiome	1065
chr17:8,189,376–8,190,688	305.5 kb	Distal (>10kb) Multiome	748

Genome Browser

Genomic view of the CHD3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.