The protein encoded by this gene plays a central role in the regulation of circadian rhythms. The protein encodes a transcription factor of the basic helix-loop-helix (bHLH) family and contains DNA binding histone acetyltransferase activity. The encoded protein forms a heterodimer with ARNTL (BMAL1) that binds E-box enhancer elements upstream of Period (PER1, PER2, PER3) and Cryptochrome (CRY1, CRY2) genes and activates transcription of these genes. PER and CRY proteins heterodimerize and repress their own transcription by interacting in a feedback loop with CLOCK/ARNTL complexes. Polymorphisms in this gene may be associated with behavioral changes in certain populations and with obesity and metabolic syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Transcription factors with Perturb-seq knockdown data for CLOCK. 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 = CLOCK 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 CLOCK, 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 |
|---|---|---|---|---|
| chr4:55,256,726–55,257,189 | 289.9 kb | Distal (>10kb) Multiome | 74 | |
| chr4:55,280,261–55,281,766 | 265.5 kb | Distal (>10kb) Multiome | 162 | |
| chr4:55,346,084–55,347,178 | 200.5 kb | Distal (>10kb) Multiome | 874 | |
| chr4:55,395,297–55,396,739 | 151.1 kb | Distal (>10kb) Multiome | 882 | |
| chr4:55,545,595–55,547,586 | 113 bp | At TSS Multiome | 933 | |
| chr4:55,635,259–55,636,954 | 89.4 kb | Distal (>10kb) Multiome | 468 | |
| chr4:55,675,062–55,675,981 | 128.6 kb | Distal (>10kb) Multiome | 89 | |
| chr4:55,676,969–55,678,075 | 130.4 kb | Distal (>10kb) Multiome | 12 |
Genomic view of the CLOCK 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.