Table 3.
cis-eQTLs located in upstream intergenic regions linked with methylation in Lineage 4 strains.
| Gene | Position | strand | Motif | Distance from start codon (bp) | Promoter/TSS | Regulation in non-methylated samples |
|---|---|---|---|---|---|---|
| Rv0565c | 657533 | − | CTGGAG | −63 | − | Down |
| ompA | 1002711 | + | CTCCAG | −101 | − | Down |
| Rv1371 | 1543277 | + | CTCCAG | −82 | − | Up |
| scpB | 1938088 | + | CTCCAG | −58 | P, TSS | Up |
| moaC3 | 3710411 | − | CTCCAG | −163 | − | Up |
| Rv3324A | 3710411 | − | CTCCAG | −32 | − | Up |
| Rv3325 | 3710408 | + | CTGGAG | −25 | − | Down |
| PE_PGRS60 | 4093563 | + | CTGGAG | −69 | − | Down |
Table showing genes differentially expressed potentially due to the lack of methylation in the upstream region. The name of the gene, the position of the eQTL (methylation site), strand, motif, distance of the methylated base from start codon of the transcript (negative shown as upstream), prediction of promoter or TSS (P = promoter region, TSS = Transcriptional Start Site), and type of regulation of the gene in non-methylated samples is shown.