Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. This gene encodes a centromere protein which contains a histone H3 related histone fold domain that is required for targeting to the centromere. Centromere protein A is proposed to be a component of a modified nucleosome or nucleosome-like structure in which it replaces 1 or both copies of conventional histone H3 in the (H3-H4)2 tetrameric core of the nucleosome particle. The protein is a replication-independent histone that is a member of the histone H3 family. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Nov 2015]
Transcription factors with Perturb-seq knockdown data for CENPA. 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 = CENPA 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 CENPA, 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 |
|---|---|---|---|---|
| chr2:26,503,215–26,503,885 | 260.7 kb | Distal (>10kb) Multiome | 522 | |
| chr2:26,591,548–26,592,367 | 172.2 kb | Distal (>10kb) Multiome HiCAR | 47 | |
| chr2:26,692,280–26,693,600 | 71.5 kb | Distal (>10kb) Multiome | 275 | |
| chr2:26,749,944–26,750,505 | 14.1 kb | Distal (>10kb) Multiome | 322 | |
| chr2:26,758,065–26,758,323 | 6.0 kb | Proximal (<10kb) | 470 | |
| chr2:26,764,126–26,764,575 | 5 bp | At TSS Multiome | 781 | |
| chr2:26,785,402–26,786,601 | 21.6 kb | Distal (>10kb) Multiome | 996 | |
| chr2:26,846,388–26,846,855 | 82.2 kb | Distal (>10kb) Multiome | 343 | |
| chr2:26,847,436–26,849,494 | 83.7 kb | Distal (>10kb) Multiome | 447 | |
| chr2:26,961,589–26,962,066 | 197.6 kb | Distal (>10kb) Multiome | 502 | |
| chr2:26,970,294–26,971,331 | 206.3 kb | Distal (>10kb) Multiome | 572 | |
| chr2:27,032,577–27,033,271 | 268.6 kb | Distal (>10kb) Multiome | 799 | |
| chr2:27,049,564–27,052,299 | 286.5 kb | Distal (>10kb) Multiome | 1295 |
Genomic view of the CENPA 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.