O/E sites define the OR TSS. (A) OR promoters (n = 1085 for O/E, 243 for TBP) and (B) GC-rich promoters (≥65% GC in −750 to +250 region; n = 1098) were searched for O/E and TBP sites using strings. (O/E) TCCCTGGGG, up to one mismatch; (TBP) TATAWW. Sites were plotted by position relative to TSS. (C,D) Murine promoters were filtered by H4K20-Me3 (“TK20”) coverage of at least 50% of the gene body, then by AT content of at least 60%, and then by presence of summary O/E site (TCCC or CCCT string) within 100 bp upstream of the TSS. Of 501 murine promoters meeting the filters, 383 drive ORs (specificity: 78%; sensitivity: 38%). The numbers of genes passing each filter and statistical significance can be found in Supplemental Table S3. (E) Gibbs Recursive Sampler and MEME identify new O/E sites in OR promoters.
