H2AX

H2A.X variant histone | H2AFX

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene encodes a replication-independent histone that is a member of the histone H2A family, and generates two transcripts through the use of the conserved stem-loop termination motif, and the polyA addition motif. [provided by RefSeq, Oct 2015]

Member of: DE-11 DE-11.1

Biological processes 43 terms

DNA binding (GO:0003677)DNA binding (GO:0003677)DNA damage checkpoint signaling (GO:0000077)DNA damage response (GO:0006974)DNA damage response (GO:0006974)DNA damage response (GO:0006974)XY body (GO:0001741)centrosome (GO:0005813)chromatin (GO:0000785)chromatin-protein adaptor activity (GO:0140463)chromosome (GO:0005694)chromosome, telomeric region (GO:0000781)condensed nuclear chromosome (GO:0000794)damaged DNA binding (GO:0003684)double-strand break repair (GO:0006302)enzyme binding (GO:0019899)extracellular exosome (GO:0070062)heterochromatin formation (GO:0031507)histone binding (GO:0042393)male germ cell nucleus (GO:0001673)nuclear speck (GO:0016607)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome assembly (GO:0006334)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA repair (GO:0045739)protein binding (GO:0005515)protein heterodimerization activity (GO:0046982)protein localization to site of double-strand break (GO:1990166)replication fork (GO:0005657)response to ionizing radiation (GO:0010212)site of DNA damage (GO:0090734)site of double-strand break (GO:0035861)site of double-strand break (GO:0035861)site of double-strand break (GO:0035861)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)

Expression (TPM)

TFs regulating H2AX 0 TFs

Transcription factors with Perturb-seq knockdown data for H2AX. 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 = H2AX 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 H2AX

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H2AX, 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
chr11:118,907,074–118,907,685	188.2 kb	Distal (>10kb) Multiome	491
chr11:118,909,181–118,909,816	186.1 kb	Distal (>10kb) Multiome	326
chr11:118,909,976–118,911,609	184.8 kb	Distal (>10kb) Multiome	652
chr11:118,911,717–118,912,963	183.2 kb	Distal (>10kb) Multiome	689
chr11:118,916,429–118,917,335	178.5 kb	Distal (>10kb) Multiome	355
chr11:118,917,640–118,918,851	177.0 kb	Distal (>10kb) Multiome	522
chr11:118,925,703–118,926,356	169.4 kb	Distal (>10kb) Multiome	595
chr11:118,927,947–118,930,852	166.0 kb	Distal (>10kb) Multiome	892
chr11:118,997,538–118,998,797	97.4 kb	Distal (>10kb) Multiome	798
chr11:119,018,081–119,019,265	76.9 kb	Distal (>10kb) Multiome	897
chr11:119,029,885–119,031,330	64.6 kb	Distal (>10kb) Multiome	876
chr11:119,056,436–119,057,778	38.2 kb	Distal (>10kb) Multiome	815
chr11:119,067,446–119,068,100	27.7 kb	Distal (>10kb) Multiome	762
chr11:119,084,563–119,085,756	10.4 kb	Distal (>10kb) Multiome	846
chr11:119,093,969–119,096,070	98 bp	At TSS Multiome	1046
chr11:119,101,351–119,102,791	6.7 kb	Proximal (<10kb) Multiome	871
chr11:119,106,906–119,107,993	11.9 kb	Distal (>10kb) Multiome	650
chr11:119,120,857–119,122,037	26.0 kb	Distal (>10kb) Multiome	787
chr11:119,144,795–119,145,355	49.6 kb	Distal (>10kb) Multiome	230
chr11:119,148,816–119,149,933	54.1 kb	Distal (>10kb) Multiome	262
chr11:119,168,601–119,169,645	73.4 kb	Distal (>10kb) Multiome	794
chr11:119,205,241–119,207,150	110.7 kb	Distal (>10kb) Multiome	695
chr11:119,315,017–119,315,819	219.9 kb	Distal (>10kb) Multiome HiCAR	270
chr11:119,316,693–119,317,760	221.7 kb	Distal (>10kb) Multiome HiCAR	463
chr11:119,320,617–119,321,906	226.3 kb	Distal (>10kb) Multiome	516
chr11:119,334,140–119,334,815	238.9 kb	Distal (>10kb) Multiome	577
chr11:119,337,716–119,338,797	242.8 kb	Distal (>10kb) Multiome	412
chr11:119,339,587–119,340,902	244.7 kb	Distal (>10kb) Multiome	477
chr11:119,356,332–119,357,013	261.3 kb	Distal (>10kb) Multiome	366
chr11:119,361,041–119,361,699	265.9 kb	Distal (>10kb) Multiome	431
chr11:119,363,939–119,364,561	268.8 kb	Distal (>10kb) Multiome	255
chr11:119,377,954–119,379,307	283.1 kb	Distal (>10kb) Multiome	307
chr11:119,380,894–119,382,060	286.2 kb	Distal (>10kb) Multiome	800

Genome Browser

Genomic view of the H2AX 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.