The location of the obtained motifs in the tested gene set promoters was visualized by the Motif Align and Search Tool (MAST) within the MEME software suite [48].
Veerla et al. recently developed SMART software for identifying co-occurring TFBSs in gene set promoters [ 7].
Using this method to edit the GAL1 and GAL80 promoter sequences, we found that the relative positioning of promoter elements was critically important for setting promoter activity levels in single cells.
Moreover, the number of c-Myc binding sites identified in the promoter set including promoters of induced genes was compared to the number of c-Myc binding sites identified in the control promoter set.
The average distance between TE insertions and the TSS did not vary significantly among promoter sets (mean Promoter set I: 479 bp; Promoter set II: 515 bp; Promoter set III: 451 bp; Mann-Whitney U-test, I vs. II: p = 0.704, I vs. III: p = 0.624, II vs. III: p = 0.337).
As co-MYC regions showed a strong tendency to be located close to annotated TSSs we termed this enhancer negative training set promoter-like (PrL, see Methods).
We produced the "universe" set of promoters for a given epigenetic mark by forming, for each epigenetic mark, the union of positive promoters across BTSC types.
The latter sets deviate from a Poisson distribution (12 species hsp70: chi-square, p<0.0001, Hsp70 in D. melanogaster natural populations: p<0.0001; Set I promoters in D. melanogaster natural populations, p<0.0001), whereas those inserting into the genesets for the 12 species do not (Promoter set I: p = 0.743, Promoter set II: p = 0.279, Promoter set III: p = 0.272).
This can happen, for example, when the small input set of promoters all happen to be AT rich.
(1) We identified a "core set" of promoters possessing each epigenetic mark in every surveyed BTSC cell type.
Promoter set II comprises 324 340 kB of promoter sequence, and harbors 24 insertions or 70 74 per mB.
