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 encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for ATG4B. 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 = ATG4B 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 ATG4B, 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 |
|---|---|---|---|---|
| chr2:241,354,545–241,355,644 | 282.7 kb | Distal (>10kb) Multiome | 625 | |
| chr2:241,355,946–241,356,875 | 281.5 kb | Distal (>10kb) Multiome | 680 | |
| chr2:241,507,257–241,509,444 | 129.0 kb | Distal (>10kb) Multiome | 1050 | |
| chr2:241,540,846–241,542,485 | 96.4 kb | Distal (>10kb) Multiome | 394 | |
| chr2:241,558,542–241,559,899 | 78.9 kb | Distal (>10kb) Multiome | 638 | |
| chr2:241,609,833–241,610,860 | 27.3 kb | Distal (>10kb) Multiome | 755 | |
| chr2:241,636,378–241,638,145 | 295 bp | At TSS Multiome | 934 | |
| chr2:241,686,350–241,687,468 | 49.2 kb | Distal (>10kb) Multiome | 895 | |
| chr2:241,701,038–241,703,402 | 63.7 kb | Distal (>10kb) Multiome | 1081 | |
| chr2:241,734,032–241,735,695 | 96.9 kb | Distal (>10kb) Multiome | 977 | |
| chr2:241,843,948–241,844,465 | 206.5 kb | Distal (>10kb) Multiome | 429 | |
| chr2:241,880,851–241,882,624 | 244.0 kb | Distal (>10kb) Multiome | 665 |
Genomic view of the ATG4B 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.