HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator Tat is dependent on an RNA regulatory element (TAR) located downstream of the transcription initiation site. The protein encoded by this gene is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. A similar pseudogene is present on chromosome 20. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for TARDBP. 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 = TARDBP 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 TARDBP, 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 |
|---|---|---|---|---|
| chr1:10,793,659–10,795,336 | 218.7 kb | Distal (>10kb) Multiome | 450 | |
| chr1:10,796,172–10,796,997 | 216.0 kb | Distal (>10kb) Multiome | 574 | |
| chr1:10,835,650–10,836,437 | 176.6 kb | Distal (>10kb) Multiome | 422 | |
| chr1:10,866,886–10,867,599 | 145.4 kb | Distal (>10kb) Multiome | 364 | |
| chr1:11,011,823–11,013,364 | 210 bp | At TSS Multiome | 974 | |
| chr1:11,052,805–11,053,698 | 40.6 kb | Distal (>10kb) Multiome | 314 | |
| chr1:11,059,469–11,060,508 | 47.4 kb | Distal (>10kb) Multiome | 659 | |
| chr1:11,099,300–11,100,191 | 87.1 kb | Distal (>10kb) Multiome | 798 | |
| chr1:11,262,158–11,262,957 | 250.0 kb | Distal (>10kb) Multiome | 805 | |
| chr1:11,272,615–11,274,143 | 260.5 kb | Distal (>10kb) Multiome | 912 | |
| chr1:11,311,832–11,312,672 | 299.6 kb | Distal (>10kb) Multiome | 49 |
Genomic view of the TARDBP 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.