This gene encodes a member of the muscle segment homeobox gene family. The encoded protein functions as a transcriptional repressor during embryogenesis through interactions with components of the core transcription complex and other homeoproteins. It may also have roles in limb-pattern formation, craniofacial development, particularly odontogenesis, and tumor growth inhibition. Mutations in this gene, which was once known as homeobox 7, have been associated with nonsyndromic cleft lip with or without cleft palate 5, Witkop syndrome, Wolf-Hirschom syndrome, and autosomoal dominant hypodontia. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for MSX1. 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 = MSX1 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 MSX1, 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 |
|---|---|---|---|---|
| chr4:4,852,426–4,853,033 | 6.6 kb | Proximal (<10kb) | 161 | |
| chr4:4,854,580–4,855,148 | 4.5 kb | Proximal (<10kb) | 69 | |
| chr4:4,856,179–4,857,204 | 2.5 kb | Proximal (<10kb) | 224 | |
| chr4:4,857,851–4,858,461 | 1.2 kb | Proximal (<10kb) | 75 | |
| chr4:4,859,270–4,860,814 | at TSS | At TSS | 635 | |
| chr4:4,860,908–4,861,424 | 1.2 kb | Proximal (<10kb) | 199 | |
| chr4:4,862,719–4,863,094 | 3.1 kb | Proximal (<10kb) | 70 | |
| chr4:4,866,173–4,866,537 | 6.5 kb | Proximal (<10kb) | 68 | |
| chr4:4,867,206–4,867,764 | 7.5 kb | Proximal (<10kb) | 95 |
Genomic view of the MSX1 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.