HLA-E belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. HLA-E binds a restricted subset of peptides derived from the leader peptides of other class I molecules. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for HLA-E. 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 = HLA-E 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 HLA-E, 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 |
|---|---|---|---|---|
| chr6:30,207,044–30,207,811 | 282.1 kb | Distal (>10kb) Multiome | 514 | |
| chr6:30,212,953–30,213,888 | 276.0 kb | Distal (>10kb) Multiome | 826 | |
| chr6:30,213,977–30,214,728 | 274.9 kb | Distal (>10kb) Multiome | 758 | |
| chr6:30,259,131–30,260,199 | 230.0 kb | Distal (>10kb) Multiome | 475 | |
| chr6:30,325,606–30,327,611 | 162.5 kb | Distal (>10kb) Multiome | 1043 | |
| chr6:30,344,843–30,345,715 | 144.3 kb | Distal (>10kb) Multiome | 892 | |
| chr6:30,357,696–30,358,238 | 131.6 kb | Distal (>10kb) Multiome | 207 | |
| chr6:30,466,230–30,466,713 | 23.0 kb | Distal (>10kb) Multiome | 369 | |
| chr6:30,482,109–30,482,343 | 7.2 kb | Proximal (<10kb) | 220 | |
| chr6:30,489,117–30,490,512 | 808 bp | At TSS Multiome | 750 | |
| chr6:30,516,006–30,516,707 | 26.8 kb | Distal (>10kb) Multiome | 739 | |
| chr6:30,555,407–30,557,765 | 67.1 kb | Distal (>10kb) Multiome HiCAR | 1161 | |
| chr6:30,570,822–30,571,949 | 81.9 kb | Distal (>10kb) Multiome HiCAR | 1000 | |
| chr6:30,614,393–30,615,939 | 125.7 kb | Distal (>10kb) Multiome | 837 | |
| chr6:30,616,770–30,618,155 | 128.0 kb | Distal (>10kb) Multiome | 1072 | |
| chr6:30,626,560–30,627,206 | 137.3 kb | Distal (>10kb) Multiome | 802 | |
| chr6:30,646,505–30,648,035 | 157.8 kb | Distal (>10kb) Multiome | 961 | |
| chr6:30,672,571–30,673,266 | 183.5 kb | Distal (>10kb) Multiome | 812 | |
| chr6:30,679,032–30,679,479 | 189.7 kb | Distal (>10kb) Multiome | 603 | |
| chr6:30,686,268–30,688,032 | 197.7 kb | Distal (>10kb) Multiome | 801 | |
| chr6:30,690,445–30,691,240 | 201.5 kb | Distal (>10kb) Multiome | 644 | |
| chr6:30,716,986–30,717,874 | 228.0 kb | Distal (>10kb) Multiome | 1059 | |
| chr6:30,719,428–30,720,577 | 230.7 kb | Distal (>10kb) Multiome | 724 | |
| chr6:30,721,307–30,722,103 | 232.0 kb | Distal (>10kb) Multiome | 872 | |
| chr6:30,725,731–30,726,564 | 236.7 kb | Distal (>10kb) Multiome | 478 | |
| chr6:30,740,996–30,745,094 | 253.2 kb | Distal (>10kb) Multiome | 1233 | |
| chr6:30,763,647–30,765,193 | 274.9 kb | Distal (>10kb) Multiome | 850 |
Genomic view of the HLA-E 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.