GATAD2B

GATA zinc finger domain containing 2B | P66beta

This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016]

Member of: DE-2 DE-2.1 Developmental clusters: GC7 GC2

Biological processes 26 terms

DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)NuRD complex (GO:0016581)NuRD complex (GO:0016581)chromatin (GO:0000785)chromatin remodeling (GO:0006338)chromatin remodeling (GO:0006338)chromatin remodeling (GO:0006338)chromosome (GO:0005694)chromosome, telomeric region (GO:0000781)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)nuclear speck (GO:0016607)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleosomal DNA binding (GO:0031492)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)protein binding (GO:0005515)protein-containing complex (GO:0032991)regulation of DNA-templated transcription (GO:0006355)regulation of cell fate specification (GO:0042659)regulation of stem cell differentiation (GO:2000736)sequence-specific DNA binding (GO:0043565)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating GATAD2B 0 TFs

Transcription factors with Perturb-seq knockdown data for GATAD2B. 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 = GATAD2B 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 GATAD2B

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of GATAD2B, 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
chr1:153,626,535–153,627,974	295.4 kb	Distal (>10kb) Multiome	697
chr1:153,633,575–153,634,639	288.8 kb	Distal (>10kb) Multiome	998
chr1:153,658,331–153,659,230	264.2 kb	Distal (>10kb) Multiome	746
chr1:153,670,709–153,671,992	251.8 kb	Distal (>10kb) Multiome	884
chr1:153,697,776–153,698,654	224.6 kb	Distal (>10kb) Multiome	313
chr1:153,727,492–153,728,827	195.1 kb	Distal (>10kb) Multiome	702
chr1:153,736,782–153,737,426	185.9 kb	Distal (>10kb) Multiome	10
chr1:153,745,487–153,745,959	177.3 kb	Distal (>10kb) Multiome	55
chr1:153,774,962–153,776,698	147.8 kb	Distal (>10kb) Multiome	671
chr1:153,783,341–153,784,300	139.3 kb	Distal (>10kb) Multiome HiCAR	794
chr1:153,922,213–153,923,779	91 bp	At TSS Multiome	856
chr1:153,945,717–153,947,118	23.7 kb	Distal (>10kb) Multiome	866
chr1:153,957,828–153,959,103	35.7 kb	Distal (>10kb) Multiome	912
chr1:153,963,107–153,964,407	40.7 kb	Distal (>10kb) Multiome	798
chr1:153,967,147–153,968,324	44.7 kb	Distal (>10kb) Multiome	986
chr1:153,977,057–153,978,034	54.7 kb	Distal (>10kb) Multiome	853
chr1:153,985,902–153,987,184	63.5 kb	Distal (>10kb) Multiome	572
chr1:153,990,402–153,991,082	67.8 kb	Distal (>10kb) Multiome	950
chr1:154,182,339–154,183,774	260.4 kb	Distal (>10kb) Multiome	934
chr1:154,220,079–154,221,864	297.8 kb	Distal (>10kb) Multiome	1071

Genome Browser

Genomic view of the GATAD2B 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.