This gene encodes a protein that belongs to the High Mobility Group-box superfamily. The encoded non-histone, nuclear DNA-binding protein regulates transcription, and is involved in organization of DNA. This protein plays a role in several cellular processes, including inflammation, cell differentiation and tumor cell migration. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2015]
Transcription factors with Perturb-seq knockdown data for HMGB1. 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 = HMGB1 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 HMGB1, 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 |
|---|---|---|---|---|
| chr13:30,182,219–30,182,971 | 283.4 kb | Distal (>10kb) Multiome | 134 | |
| chr13:30,306,729–30,307,939 | 158.8 kb | Distal (>10kb) Multiome | 756 | |
| chr13:30,408,104–30,408,932 | 57.4 kb | Distal (>10kb) Multiome | 692 | |
| chr13:30,421,116–30,422,727 | 43.7 kb | Distal (>10kb) Multiome | 513 | |
| chr13:30,445,442–30,446,304 | 20.1 kb | Distal (>10kb) Multiome | 484 | |
| chr13:30,464,236–30,465,228 | 1.2 kb | Proximal (<10kb) Multiome | 645 | |
| chr13:30,465,545–30,466,629 | 116 bp | At TSS Multiome | 658 | |
| chr13:30,616,955–30,618,550 | 151.8 kb | Distal (>10kb) Multiome HiCAR | 1201 | |
| chr13:30,673,480–30,674,640 | 208.3 kb | Distal (>10kb) Multiome | 857 | |
| chr13:30,740,081–30,740,925 | 274.6 kb | Distal (>10kb) Multiome | 313 | |
| chr13:30,756,867–30,757,734 | 291.4 kb | Distal (>10kb) Multiome | 123 |
Genomic view of the HMGB1 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.