This gene encodes a DNA-binding protein which has high specificity for scaffold or matrix attachment region DNA elements (S/MAR DNA). This protein is thought to be involved in attaching the base of chromatin loops to the nuclear matrix but there is conflicting evidence as to whether this protein is a component of chromatin or a nuclear matrix protein. Scaffold attachment factors are a specific subset of nuclear matrix proteins (NMP) that specifically bind to S/MAR. The encoded protein is thought to serve as a molecular base to assemble a 'transcriptosome complex' in the vicinity of actively transcribed genes. It is involved in the regulation of heat shock protein 27 transcription, can act as an estrogen receptor co-repressor and is a candidate for breast tumorigenesis. This gene is arranged head-to-head with a similar gene whose product has the same functions. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]
Transcription factors with Perturb-seq knockdown data for SAFB. 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 = SAFB 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 SAFB, 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 |
|---|---|---|---|---|
| chr19:4,534,817–4,535,416 | 1087.9 kb | Distal (>10kb) Multiome HiCAR | 451 | |
| chr19:5,339,639–5,341,408 | 282.2 kb | Distal (>10kb) Multiome | 966 | |
| chr19:5,397,820–5,398,866 | 224.7 kb | Distal (>10kb) Multiome | 137 | |
| chr19:5,436,304–5,437,277 | 186.3 kb | Distal (>10kb) Multiome | 227 | |
| chr19:5,536,326–5,536,869 | 86.4 kb | Distal (>10kb) Multiome | 306 | |
| chr19:5,567,504–5,568,201 | 55.3 kb | Distal (>10kb) Multiome | 209 | |
| chr19:5,585,656–5,586,338 | 37.1 kb | Distal (>10kb) Multiome | 267 | |
| chr19:5,621,964–5,623,739 | 155 bp | At TSS Multiome | 857 | |
| chr19:5,679,757–5,681,464 | 57.7 kb | Distal (>10kb) Multiome | 884 | |
| chr19:5,686,329–5,687,994 | 63.9 kb | Distal (>10kb) Multiome | 693 | |
| chr19:5,689,735–5,690,874 | 67.2 kb | Distal (>10kb) Multiome | 960 | |
| chr19:5,719,717–5,721,174 | 97.3 kb | Distal (>10kb) Multiome | 985 | |
| chr19:5,790,527–5,791,509 | 167.8 kb | Distal (>10kb) Multiome | 965 | |
| chr19:5,803,750–5,806,128 | 182.1 kb | Distal (>10kb) Multiome | 858 | |
| chr19:5,826,528–5,829,726 | 205.0 kb | Distal (>10kb) Multiome | 1037 | |
| chr19:5,903,474–5,905,358 | 281.5 kb | Distal (>10kb) Multiome | 1027 |
Genomic view of the SAFB 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.