The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PRDM16. 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 = PRDM16 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 PRDM16, 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 |
|---|---|---|---|---|
| chr1:3,424,751–3,425,009 | at TSS | At TSS | 260 | |
| chr1:3,431,340–3,431,517 | 6.4 kb | Proximal (<10kb) | 100 | |
| chr1:3,453,034–3,455,700 | 29.8 kb | Distal (>10kb) Multiome | 874 | |
| chr1:3,491,285–3,491,949 | 66.6 kb | Distal (>10kb) Multiome | 309 | |
| chr1:3,530,504–3,532,073 | 106.5 kb | Distal (>10kb) Multiome | 442 | |
| chr1:3,610,667–3,612,281 | 186.7 kb | Distal (>10kb) Multiome | 361 | |
| chr1:3,624,289–3,625,883 | 200.0 kb | Distal (>10kb) Multiome | 814 | |
| chr1:3,649,785–3,650,304 | 225.1 kb | Distal (>10kb) Multiome | 620 | |
| chr1:3,651,921–3,653,136 | 227.9 kb | Distal (>10kb) Multiome | 369 |
Genomic view of the PRDM16 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.