Control of transcription by RNA polymerase II involves the basal transcription machinery which is a collection of proteins. These proteins with RNA polymerase II, assemble into complexes which are modulated by transactivator proteins that bind to cis-regulatory elements located adjacent to the transcription start site. Some modulators interact directly with the basal complex, whereas others may act as bridging proteins linking transactivators to the basal transcription factors. Some of these associated factors are weakly attached while others are tightly associated with TBP in the TFIID complex. Among the latter are the TAF proteins. Different TAFs are predicted to mediate the function of distinct transcriptional activators for a variety of gene promoters and RNA polymerases. TAF12 interacts directly with TBP as well as with TAF2I. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2008]
Transcription factors with Perturb-seq knockdown data for TAF12. 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 = TAF12 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 TAF12, 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 |
|---|---|---|---|---|
| chr1:28,369,387–28,370,499 | 273.3 kb | Distal (>10kb) Multiome | 961 | |
| chr1:28,505,412–28,506,885 | 137.1 kb | Distal (>10kb) Multiome | 969 | |
| chr1:28,513,136–28,516,505 | 127.6 kb | Distal (>10kb) Multiome | 461 | |
| chr1:28,517,302–28,519,364 | 124.7 kb | Distal (>10kb) Multiome | 927 | |
| chr1:28,552,370–28,553,806 | 90.1 kb | Distal (>10kb) Multiome | 955 | |
| chr1:28,580,985–28,582,501 | 61.2 kb | Distal (>10kb) Multiome | 1080 | |
| chr1:28,592,018–28,592,768 | 50.7 kb | Distal (>10kb) Multiome | 394 | |
| chr1:28,642,403–28,643,726 | 92 bp | At TSS Multiome | 980 | |
| chr1:28,648,003–28,650,002 | 5.8 kb | Proximal (<10kb) Multiome | 1377 | |
| chr1:28,667,742–28,669,783 | 25.3 kb | Distal (>10kb) Multiome | 804 | |
| chr1:28,736,098–28,738,080 | 93.6 kb | Distal (>10kb) Multiome | 1106 | |
| chr1:28,811,880–28,812,661 | 169.2 kb | Distal (>10kb) Multiome | 219 | |
| chr1:28,881,894–28,882,433 | 239.2 kb | Distal (>10kb) Multiome | 615 | |
| chr1:28,886,723–28,888,425 | 245.1 kb | Distal (>10kb) Multiome | 709 | |
| chr1:28,913,920–28,915,470 | 271.4 kb | Distal (>10kb) Multiome | 738 |
Genomic view of the TAF12 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.