A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the bare lymphocyte syndrome (BLS; MIM 209920). At least 4 complementation groups have been identified in B-cell lines established from patients with BLS. The molecular defects in complementation groups B, C, and D all lead to a deficiency in RFX, a nuclear protein complex that binds to the X box of MHC-II promoters. The lack of RFX binding activity in complementation group C results from mutations in the RFX5 gene encoding the 75-kD subunit of RFX (Steimle et al., 1995). RFX5 is the fifth member of the growing family of DNA-binding proteins sharing a novel and highly characteristic DNA-binding domain called the RFX motif. Multiple alternatively spliced transcript variants have been found but the full-length natures of only two have been determined. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for RFX5. 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 = RFX5 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 RFX5, 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 |
|---|---|---|---|---|
| chr1:151,047,405–151,048,764 | 298.7 kb | Distal (>10kb) Multiome | 714 | |
| chr1:151,059,187–151,059,842 | 287.6 kb | Distal (>10kb) Multiome | 821 | |
| chr1:151,060,204–151,060,723 | 286.7 kb | Distal (>10kb) Multiome | 346 | |
| chr1:151,070,369–151,071,463 | 276.1 kb | Distal (>10kb) Multiome | 835 | |
| chr1:151,131,105–151,132,256 | 215.8 kb | Distal (>10kb) Multiome | 247 | |
| chr1:151,145,115–151,147,333 | 200.5 kb | Distal (>10kb) Multiome | 709 | |
| chr1:151,165,133–151,166,350 | 181.4 kb | Distal (>10kb) Multiome | 940 | |
| chr1:151,189,687–151,190,378 | 157.1 kb | Distal (>10kb) Multiome | 875 | |
| chr1:151,198,185–151,199,073 | 148.7 kb | Distal (>10kb) Multiome | 721 | |
| chr1:151,254,421–151,255,083 | 92.5 kb | Distal (>10kb) Multiome | 770 | |
| chr1:151,281,008–151,283,557 | 65.9 kb | Distal (>10kb) Multiome | 1121 | |
| chr1:151,327,019–151,328,343 | 19.6 kb | Distal (>10kb) Multiome | 719 | |
| chr1:151,340,951–151,341,150 | 5.7 kb | Proximal (<10kb) | 300 | |
| chr1:151,346,796–151,347,793 | 34 bp | At TSS Multiome | 711 | |
| chr1:151,399,359–151,400,043 | 52.3 kb | Distal (>10kb) Multiome | 776 | |
| chr1:151,458,247–151,459,879 | 112.2 kb | Distal (>10kb) Multiome | 796 | |
| chr1:151,491,747–151,492,512 | 144.9 kb | Distal (>10kb) Multiome | 146 | |
| chr1:151,502,459–151,503,303 | 155.6 kb | Distal (>10kb) Multiome | 99 | |
| chr1:151,510,863–151,512,136 | 164.1 kb | Distal (>10kb) Multiome | 640 | |
| chr1:151,539,661–151,541,320 | 193.0 kb | Distal (>10kb) Multiome | 830 | |
| chr1:151,611,789–151,613,070 | 264.8 kb | Distal (>10kb) Multiome | 761 |
Genomic view of the RFX5 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.