Figure 2: DNase I footprints mark sites of in vivo protein occupancy.
From: An expansive human regulatory lexicon encoded in transcription factor footprints
a, Schematic and plots showing the effect of T/C SNV rs4144593 on protein occupancy and chromatin accessibility. The y axis of the bar graph shows the number of DNase I cleavage events containing either the T or C allele. Middle plots show T or C allele-specific DNase I cleavage profiles from ten cell lines heterozygous for the T/C alleles at rs4144593. Right plots show DNase I cleavage profiles from 18 cell lines homozygous for the C allele at rs4144593 and one cell line homozygous for the T allele at rs4144593. Cleavage plots are cut off at 60% cleavage height. b, The average CpG methylation within IMR90 DNase I footprints, IMR90 DHSs (but not in footprints) and non-hypersensitive genomic regions in IMR90 cells. CpG methylation is significantly depleted in DNase I footprints (P < 2.2 × 10−16, MannWhitney U-test).
