This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
Transcription factors with Perturb-seq knockdown data for TCOF1. 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 = TCOF1 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 TCOF1, 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 |
|---|---|---|---|---|
| chr5:150,130,018–150,131,367 | 226.9 kb | Distal (>10kb) Multiome | 516 | |
| chr5:150,161,225–150,162,105 | 196.0 kb | Distal (>10kb) Multiome | 389 | |
| chr5:150,211,110–150,211,964 | 146.2 kb | Distal (>10kb) Multiome | 131 | |
| chr5:150,302,023–150,303,433 | 54.9 kb | Distal (>10kb) Multiome | 377 | |
| chr5:150,350,539–150,350,849 | 6.9 kb | Proximal (<10kb) | 555 | |
| chr5:150,357,249–150,358,378 | 75 bp | At TSS Multiome | 746 | |
| chr5:150,409,825–150,410,350 | 52.3 kb | Distal (>10kb) Multiome | 299 | |
| chr5:150,412,530–150,413,063 | 55.1 kb | Distal (>10kb) Multiome | 495 | |
| chr5:150,441,289–150,442,097 | 83.9 kb | Distal (>10kb) Multiome | 188 | |
| chr5:150,449,356–150,450,212 | 92.2 kb | Distal (>10kb) Multiome | 1068 | |
| chr5:150,458,741–150,459,365 | 101.3 kb | Distal (>10kb) Multiome | 430 | |
| chr5:150,485,401–150,487,150 | 128.1 kb | Distal (>10kb) Multiome | 761 | |
| chr5:150,577,977–150,578,481 | 220.6 kb | Distal (>10kb) Multiome | 149 | |
| chr5:150,624,424–150,625,067 | 267.1 kb | Distal (>10kb) Multiome | 250 | |
| chr5:150,656,143–150,657,405 | 299.0 kb | Distal (>10kb) Multiome | 607 |
Genomic view of the TCOF1 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.