Ubiquinone, also known as coenzyme Q, or Q, is a critical component of the electron transport pathways of both eukaryotes and prokaryotes (Jonassen and Clarke, 2000 [PubMed 10777520]). This lipid consists of a hydrophobic isoprenoid tail and a quinone head group. The tail varies in length depending on the organism, but its purpose is to anchor coenzyme Q to the membrane. The quinone head group is responsible for the activity of coenzyme Q in the respiratory chain. The S. cerevisiae COQ3 gene encodes an O-methyltransferase required for 2 steps in the biosynthetic pathway of coenzyme Q. This enzyme methylates an early coenzyme Q intermediate, 3,4-dihydroxy-5-polyprenylbenzoic acid, as well as the final intermediate in the pathway, converting demethyl-ubiquinone to coenzyme Q. The COQ3 gene product is also capable of methylating the distinct prokaryotic early intermediate 2-hydroxy-6-polyprenyl phenol.[supplied by OMIM, Mar 2008]
Transcription factors with Perturb-seq knockdown data for COQ3. 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 = COQ3 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 COQ3, 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 |
|---|---|---|---|---|
| chr6:99,219,557–99,220,312 | 174.2 kb | Distal (>10kb) Multiome | 105 | |
| chr6:99,348,770–99,350,367 | 44.4 kb | Distal (>10kb) Multiome | 615 | |
| chr6:99,393,480–99,394,529 | 185 bp | At TSS Multiome | 782 | |
| chr6:99,424,727–99,426,355 | 31.2 kb | Distal (>10kb) Multiome | 975 | |
| chr6:99,514,702–99,516,390 | 121.3 kb | Distal (>10kb) Multiome | 945 | |
| chr6:99,520,676–99,522,033 | 126.9 kb | Distal (>10kb) Multiome | 822 | |
| chr6:99,567,957–99,569,279 | 174.5 kb | Distal (>10kb) Multiome | 1064 | |
| chr6:99,588,272–99,589,608 | 194.7 kb | Distal (>10kb) Multiome | 545 | |
| chr6:99,602,753–99,604,086 | 209.5 kb | Distal (>10kb) Multiome | 376 | |
| chr6:99,612,582–99,615,086 | 219.5 kb | Distal (>10kb) Multiome | 533 | |
| chr6:99,618,513–99,619,470 | 224.7 kb | Distal (>10kb) Multiome | 225 |
Genomic view of the COQ3 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.