This gene encodes a methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C) at position 34 of intron-containing tRNA(Leu)(CAA) precursors. This modification is necessary to stabilize the anticodon-codon pairing and correctly translate the mRNA. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Mar 2011]
Transcription factors with Perturb-seq knockdown data for NSUN2. 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 = NSUN2 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 NSUN2, 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 |
|---|---|---|---|---|
| chr5:6,377,871–6,379,073 | 254.7 kb | Distal (>10kb) Multiome | 776 | |
| chr5:6,475,554–6,476,306 | 157.4 kb | Distal (>10kb) Multiome | 93 | |
| chr5:6,582,577–6,583,754 | 50.1 kb | Distal (>10kb) Multiome | 244 | |
| chr5:6,595,290–6,596,038 | 37.6 kb | Distal (>10kb) Multiome | 157 | |
| chr5:6,632,465–6,634,316 | 9 bp | At TSS Multiome | 837 | |
| chr5:6,637,424–6,638,209 | 4.4 kb | Proximal (<10kb) | 16 | |
| chr5:6,686,711–6,687,368 | 53.8 kb | Distal (>10kb) Multiome | 390 | |
| chr5:6,712,052–6,714,014 | 79.9 kb | Distal (>10kb) Multiome HiCAR | 953 | |
| chr5:6,765,540–6,766,155 | 132.5 kb | Distal (>10kb) Multiome | 329 | |
| chr5:6,818,419–6,819,319 | 185.4 kb | Distal (>10kb) Multiome | 115 | |
| chr5:7,849,610–7,851,526 | 1217.3 kb | Distal (>10kb) Multiome HiCAR | 471 |
Genomic view of the NSUN2 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.