Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is located on chromosome 12 and encodes a replication-independent histone that is a variant H2A histone. The protein is divergent at the C-terminus compared to the consensus H2A histone family member. This gene also encodes an antimicrobial peptide with antibacterial and antifungal activity.[provided by RefSeq, Oct 2015]
Transcription factors with Perturb-seq knockdown data for H2AJ. 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 = H2AJ 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 |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H2AJ, 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.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr12:14,567,263–14,568,383 | 206.6 kb | Distal (>10kb) Multiome | 366 | |
| chr12:14,710,018–14,711,213 | 63.7 kb | Distal (>10kb) Multiome HiCAR | 148 | |
| chr12:14,766,115–14,766,276 | 8.1 kb | Proximal (<10kb) | 32 | |
| chr12:14,766,378–14,766,797 | 7.6 kb | Proximal (<10kb) | 28 | |
| chr12:14,768,991–14,772,177 | 4.5 kb | Proximal (<10kb) Multiome HiCAR | 1151 | |
| chr12:14,773,064–14,773,253 | 1.1 kb | Proximal (<10kb) | 26 | |
| chr12:14,773,514–14,775,433 | 120 bp | At TSS Multiome | 550 | |
| chr12:14,802,974–14,804,269 | 29.2 kb | Distal (>10kb) Multiome HiCAR | 702 | |
| chr12:15,910,800–15,911,739 | 1136.9 kb | Distal (>10kb) Multiome HiCAR | 788 |
Genomic view of the H2AJ 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.