This gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex. Two regions of potential trinucleotide repeat expansions are present in the N-terminal region of the encoded protein, and these and other mutations in this gene have been associated with the bone development disorder cleidocranial dysplasia (CCD). Transcript variants that encode different protein isoforms result from the use of alternate promoters as well as alternate splicing. [provided by RefSeq, Jul 2016]
Transcription factors with Perturb-seq knockdown data for RUNX2. 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 = RUNX2 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 RUNX2, 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 |
|---|---|---|---|---|
| chr6:44,469,799–44,470,296 | 952.6 kb | Distal (>10kb) Multiome HiCAR | 375 | |
| chr6:44,475,548–44,476,402 | 946.6 kb | Distal (>10kb) Multiome HiCAR | 587 | |
| chr6:44,655,058–44,656,097 | 767.0 kb | Distal (>10kb) Multiome HiCAR | 531 | |
| chr6:45,377,101–45,378,585 | 44.6 kb | Distal (>10kb) Multiome | 1059 | |
| chr6:45,419,505–45,420,281 | 2.3 kb | Proximal (<10kb) | 407 | |
| chr6:45,421,479–45,424,366 | 609 bp | At TSS Multiome | 638 |
Genomic view of the RUNX2 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.