This gene encodes a member of the AF4/ lymphoid nuclear protein related to the Fragile X E syndrome (FRAXE) family of proteins, which have been implicated in human childhood lymphoblastic leukemia, fragile chromosome X intellectual disability, and ataxia. It is the prevalent mixed-lineage leukemia fusion gene associated with spontaneous acute lymphoblastic leukemia. Members of this family have three conserved domains: an N-terminal homology domain, an AF4/ lymphoid nuclear protein domain, and a C-terminal homology domain. The protein functions as a regulator of RNA polymerase II-mediated transcription through elongation and chromatin remodeling functions. Through RNA interference screens, this gene has been shown to promote the expression of CD133, a plasma membrane glycoprotein required for leukemia cell survival. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]
Transcription factors with Perturb-seq knockdown data for AFF1. 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 = AFF1 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 AFF1, 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 |
|---|---|---|---|---|
| chr4:86,891,788–86,892,917 | 42.8 kb | Distal (>10kb) Multiome | 698 | |
| chr4:86,934,199–86,936,649 | 80 bp | At TSS Multiome HiCAR | 1055 | |
| chr4:86,940,125–86,940,499 | 5.1 kb | Proximal (<10kb) | 77 | |
| chr4:86,959,519–86,960,442 | 25.0 kb | Distal (>10kb) Multiome HiCAR | 307 | |
| chr4:87,001,210–87,001,937 | 66.6 kb | Distal (>10kb) Multiome HiCAR | 141 | |
| chr4:87,006,030–87,007,611 | 72.0 kb | Distal (>10kb) Multiome HiCAR | 1004 | |
| chr4:87,010,781–87,011,212 | 3.5 kb | Proximal (<10kb) | 22 | |
| chr4:87,030,741–87,031,834 | 96.3 kb | Distal (>10kb) Multiome HiCAR | 395 | |
| chr4:87,219,648–87,221,398 | 285.6 kb | Distal (>10kb) Multiome | 820 |
Genomic view of the AFF1 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.