This gene encodes a member of the hepatoma-derived growth factor (HDGF) family. The protein includes an N-terminal PWWP domain that binds to methyl-lysine-containing histones, with specific binding of this protein to tri-methylated lysines 36 and 79 of histone H3, and di- and tri-methylated lysine 20 of histone H4. The protein functions in LEDGF/p75-independent HIV-1 replication by determining HIV-1 integration site selection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014]
Transcription factors with Perturb-seq knockdown data for HDGFL2. 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 = HDGFL2 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 HDGFL2, 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 |
|---|---|---|---|---|
| chr19:4,182,102–4,182,890 | 289.7 kb | Distal (>10kb) Multiome | 862 | |
| chr19:4,198,066–4,198,600 | 274.0 kb | Distal (>10kb) Multiome | 214 | |
| chr19:4,246,623–4,247,617 | 225.0 kb | Distal (>10kb) Multiome | 960 | |
| chr19:4,326,625–4,329,107 | 143.8 kb | Distal (>10kb) Multiome | 567 | |
| chr19:4,342,323–4,344,016 | 129.4 kb | Distal (>10kb) Multiome | 969 | |
| chr19:4,390,525–4,391,068 | 81.6 kb | Distal (>10kb) Multiome | 464 | |
| chr19:4,399,835–4,401,019 | 71.7 kb | Distal (>10kb) Multiome | 828 | |
| chr19:4,402,106–4,403,050 | 69.8 kb | Distal (>10kb) Multiome | 731 | |
| chr19:4,456,541–4,458,172 | 14.5 kb | Distal (>10kb) Multiome | 757 | |
| chr19:4,471,202–4,472,545 | 338 bp | At TSS Multiome | 715 | |
| chr19:4,474,252–4,474,874 | 2.4 kb | Proximal (<10kb) Multiome | 201 | |
| chr19:4,534,817–4,535,416 | 63.0 kb | Distal (>10kb) Multiome | 451 | |
| chr19:4,556,056–4,556,977 | 84.4 kb | Distal (>10kb) Multiome | 259 | |
| chr19:4,581,475–4,581,916 | 109.5 kb | Distal (>10kb) Multiome | 358 | |
| chr19:4,597,380–4,598,540 | 125.9 kb | Distal (>10kb) Multiome | 280 | |
| chr19:4,633,303–4,633,826 | 161.2 kb | Distal (>10kb) Multiome | 500 | |
| chr19:4,636,101–4,636,717 | 164.1 kb | Distal (>10kb) Multiome | 445 | |
| chr19:4,639,001–4,640,103 | 167.1 kb | Distal (>10kb) Multiome | 710 | |
| chr19:4,669,686–4,671,221 | 198.1 kb | Distal (>10kb) Multiome | 797 | |
| chr19:4,678,652–4,679,681 | 206.9 kb | Distal (>10kb) Multiome | 164 | |
| chr19:4,723,373–4,724,832 | 251.7 kb | Distal (>10kb) Multiome | 1021 |
Genomic view of the HDGFL2 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.