This gene encodes a basic helix-loop-helix protein expressed in various tissues. The encoded protein can interact with ARNTL or compete for E-box binding sites in the promoter of PER1 and repress CLOCK/ARNTL's transactivation of PER1. This gene is believed to be involved in the control of circadian rhythm and cell differentiation. Defects in this gene are associated with the short sleep phenotype. [provided by RefSeq, Feb 2014]
Transcription factors with Perturb-seq knockdown data for BHLHE41. 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 = BHLHE41 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 BHLHE41, 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 |
|---|---|---|---|---|
| chr12:26,113,933–26,115,170 | 9.9 kb | Proximal (<10kb) | 955 | |
| chr12:26,116,509–26,116,834 | 8.2 kb | Proximal (<10kb) | 18 | |
| chr12:26,116,898–26,117,143 | 7.9 kb | Proximal (<10kb) | 46 | |
| chr12:26,117,372–26,117,594 | 7.4 kb | Proximal (<10kb) | 36 | |
| chr12:26,121,526–26,121,694 | 3.3 kb | Proximal (<10kb) | 40 | |
| chr12:26,121,816–26,123,629 | 1.4 kb | Proximal (<10kb) | 439 | |
| chr12:26,124,811–26,126,830 | at TSS | At TSS | 661 |
Genomic view of the BHLHE41 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.