Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene belongs to the autophagy-related protein 4 (Atg4) family of C54 endopeptidases. Members of this family encode proteins that play a role in the biogenesis of autophagosomes, which sequester the cytosol and organelles for degradation by lysosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
Transcription factors with Perturb-seq knockdown data for ATG4D. 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 = ATG4D 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 ATG4D, 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 |
|---|---|---|---|---|
| chr19:10,251,723–10,252,663 | 291.9 kb | Distal (>10kb) Multiome | 969 | |
| chr19:10,269,513–10,270,051 | 274.3 kb | Distal (>10kb) Multiome | 523 | |
| chr19:10,270,913–10,271,370 | 272.8 kb | Distal (>10kb) Multiome | 753 | |
| chr19:10,286,849–10,287,511 | 256.8 kb | Distal (>10kb) Multiome | 621 | |
| chr19:10,288,709–10,290,833 | 255.0 kb | Distal (>10kb) Multiome | 688 | |
| chr19:10,292,085–10,293,198 | 251.4 kb | Distal (>10kb) Multiome | 441 | |
| chr19:10,315,359–10,316,478 | 228.0 kb | Distal (>10kb) Multiome | 830 | |
| chr19:10,332,816–10,334,107 | 210.4 kb | Distal (>10kb) Multiome | 882 | |
| chr19:10,334,573–10,335,642 | 208.9 kb | Distal (>10kb) Multiome | 584 | |
| chr19:10,352,359–10,354,435 | 191.2 kb | Distal (>10kb) Multiome | 447 | |
| chr19:10,380,209–10,381,218 | 163.2 kb | Distal (>10kb) Multiome | 874 | |
| chr19:10,403,282–10,404,914 | 140.2 kb | Distal (>10kb) Multiome | 794 | |
| chr19:10,416,245–10,417,312 | 127.2 kb | Distal (>10kb) Multiome | 988 | |
| chr19:10,417,499–10,421,409 | 123.6 kb | Distal (>10kb) Multiome | 801 | |
| chr19:10,424,198–10,424,839 | 119.4 kb | Distal (>10kb) Multiome | 563 | |
| chr19:10,431,990–10,432,435 | 111.7 kb | Distal (>10kb) Multiome | 301 | |
| chr19:10,460,915–10,461,960 | 82.6 kb | Distal (>10kb) Multiome | 340 | |
| chr19:10,502,251–10,503,615 | 41.1 kb | Distal (>10kb) Multiome | 1013 | |
| chr19:10,514,009–10,514,960 | 29.5 kb | Distal (>10kb) Multiome HiCAR | 172 | |
| chr19:10,517,347–10,518,104 | 26.1 kb | Distal (>10kb) Multiome HiCAR | 338 | |
| chr19:10,543,499–10,544,302 | 74 bp | At TSS Multiome | 617 | |
| chr19:10,552,649–10,552,827 | 8.7 kb | Proximal (<10kb) | 156 | |
| chr19:10,565,054–10,566,439 | 22.1 kb | Distal (>10kb) Multiome | 923 | |
| chr19:10,568,225–10,569,839 | 25.1 kb | Distal (>10kb) Multiome | 871 | |
| chr19:10,602,117–10,602,945 | 58.6 kb | Distal (>10kb) Multiome | 518 | |
| chr19:10,625,339–10,625,984 | 81.6 kb | Distal (>10kb) Multiome | 451 | |
| chr19:10,653,364–10,655,129 | 110.2 kb | Distal (>10kb) Multiome | 1086 | |
| chr19:10,695,264–10,696,403 | 152.0 kb | Distal (>10kb) Multiome | 831 | |
| chr19:10,701,273–10,702,291 | 157.6 kb | Distal (>10kb) Multiome | 889 | |
| chr19:10,717,121–10,718,717 | 173.9 kb | Distal (>10kb) Multiome | 849 | |
| chr19:10,835,171–10,836,835 | 292.0 kb | Distal (>10kb) Multiome | 1096 |
Genomic view of the ATG4D 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.