MHC class II gene expression is controlled primarily at the transcriptional level by transcription factors that bind to the X and Y boxes, two highly conserved elements in the proximal promoter of MHC class II genes. The protein encoded by this gene is a transcriptional repressor capable of binding to the conserved X box motif of HLA-DRA and other MHC class II genes in vitro. The protein may play a role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by IFN-gamma. Three alternative splice variants, each of which encodes a different isoform, have been identified. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for NFX1. 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 = NFX1 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 NFX1, 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 |
|---|---|---|---|---|
| chr9:33,000,845–33,002,021 | 288.9 kb | Distal (>10kb) Multiome | 802 | |
| chr9:33,024,523–33,026,243 | 265.2 kb | Distal (>10kb) Multiome | 972 | |
| chr9:33,044,108–33,044,981 | 246.0 kb | Distal (>10kb) Multiome | 451 | |
| chr9:33,076,221–33,076,965 | 213.8 kb | Distal (>10kb) Multiome | 804 | |
| chr9:33,166,320–33,168,338 | 123.1 kb | Distal (>10kb) Multiome | 849 | |
| chr9:33,171,750–33,173,178 | 117.9 kb | Distal (>10kb) Multiome | 359 | |
| chr9:33,264,068–33,265,475 | 25.7 kb | Distal (>10kb) Multiome | 790 | |
| chr9:33,267,199–33,267,770 | 23.1 kb | Distal (>10kb) Multiome | 106 | |
| chr9:33,290,056–33,291,152 | 41 bp | At TSS Multiome | 1075 | |
| chr9:33,381,203–33,381,714 | 91.0 kb | Distal (>10kb) Multiome | 134 | |
| chr9:33,415,341–33,415,979 | 125.2 kb | Distal (>10kb) Multiome | 774 | |
| chr9:33,447,056–33,448,058 | 157.1 kb | Distal (>10kb) Multiome | 547 | |
| chr9:33,452,742–33,453,295 | 162.5 kb | Distal (>10kb) Multiome | 374 | |
| chr9:33,473,593–33,474,250 | 183.5 kb | Distal (>10kb) Multiome | 635 | |
| chr9:33,515,277–33,515,972 | 225.0 kb | Distal (>10kb) Multiome | 49 | |
| chr9:33,523,393–33,524,316 | 233.2 kb | Distal (>10kb) Multiome | 303 |
Genomic view of the NFX1 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.