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 binds between the bulge and the loop of the HIV-1 TAR RNA regulatory element and activates HIV-1 gene expression in synergy with the viral Tat protein. Alternative splicing results in multiple transcript variants encoding different isoforms. This gene also has a pseudogene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for TARBP2. 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 = TARBP2 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 TARBP2, 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 |
|---|---|---|---|---|
| chr12:53,219,787–53,222,151 | 280.2 kb | Distal (>10kb) Multiome | 828 | |
| chr12:53,231,703–53,233,098 | 269.0 kb | Distal (>10kb) Multiome | 464 | |
| chr12:53,251,461–53,252,566 | 249.3 kb | Distal (>10kb) Multiome | 825 | |
| chr12:53,268,046–53,268,600 | 233.0 kb | Distal (>10kb) Multiome | 709 | |
| chr12:53,295,142–53,295,823 | 205.8 kb | Distal (>10kb) Multiome | 706 | |
| chr12:53,299,515–53,300,187 | 201.6 kb | Distal (>10kb) Multiome | 849 | |
| chr12:53,321,051–53,322,029 | 179.8 kb | Distal (>10kb) Multiome HiCAR | 935 | |
| chr12:53,324,682–53,326,037 | 176.3 kb | Distal (>10kb) Multiome HiCAR | 840 | |
| chr12:53,344,427–53,345,660 | 156.3 kb | Distal (>10kb) Multiome HiCAR | 645 | |
| chr12:53,370,910–53,371,893 | 129.9 kb | Distal (>10kb) Multiome | 861 | |
| chr12:53,378,839–53,381,297 | 120.8 kb | Distal (>10kb) Multiome | 895 | |
| chr12:53,381,689–53,382,262 | 119.2 kb | Distal (>10kb) Multiome | 264 | |
| chr12:53,421,253–53,422,044 | 79.7 kb | Distal (>10kb) Multiome | 431 | |
| chr12:53,440,979–53,441,838 | 59.7 kb | Distal (>10kb) Multiome | 779 | |
| chr12:53,451,563–53,453,067 | 49.3 kb | Distal (>10kb) Multiome | 999 | |
| chr12:53,492,147–53,494,149 | 8.2 kb | Proximal (<10kb) Multiome | 702 | |
| chr12:53,496,158–53,496,570 | 4.7 kb | Proximal (<10kb) | 188 | |
| chr12:53,498,714–53,500,111 | 1.8 kb | Proximal (<10kb) Multiome | 454 | |
| chr12:53,500,242–53,501,839 | 283 bp | At TSS Multiome | 1010 | |
| chr12:53,508,612–53,509,050 | 7.3 kb | Proximal (<10kb) | 366 | |
| chr12:53,625,664–53,626,787 | 124.9 kb | Distal (>10kb) Multiome | 880 | |
| chr12:53,675,553–53,677,839 | 174.8 kb | Distal (>10kb) Multiome | 1104 | |
| chr12:53,696,162–53,696,648 | 195.2 kb | Distal (>10kb) Multiome | 228 | |
| chr12:53,727,002–53,728,055 | 226.3 kb | Distal (>10kb) Multiome | 768 | |
| chr12:53,738,393–53,738,964 | 237.4 kb | Distal (>10kb) Multiome | 131 | |
| chr12:53,746,454–53,746,954 | 245.5 kb | Distal (>10kb) Multiome | 503 | |
| chr12:53,756,873–53,757,721 | 256.0 kb | Distal (>10kb) Multiome | 367 |
Genomic view of the TARBP2 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.