Fig. 4

SNVs at DMRs affect DNA-binding activity of a tissue-specific transcription factor. a Top 10 enriched TF motifs in B6 > C3 DSS DMRs (after expanding DMR size to a minimum of 401 bp) according to HOMER v4.9.1. b Top 10 enriched TF motifs in C3 > B6 DSS DMRs (after expanding DMR size to a minimum of 401 bp) according to HOMER v4.9.1 c Protein purification of FOXA1 DNA-binding domain (DBD). Purified FOXA1 DBD was analyzed by SDS-PAGE. The black arrow indicates FOXA1 DBD. d FOXA1 ChIP-seq signal at SNV-containing FOXA1 motifs. Occurrences of FOXA1 motifs (as defined by HOMER motifs FOXA1.LNCAP or FOXA1.MCF7) within 100 nt of a DMR were categorized by whether the B6 or C3 allele was preferred according to the HOMER position weight matrix [PWM]. FOXA1 signal in the B6 and C3 animals is reported as input-subtracted ChIP-seq read count at 100 nt regions centered on the motif occurrences. The box depicts the 25th to 75th percentiles, the black dot is the median, the whiskers extend to data points up to 1.5*IQR beyond the box, and open gray circles are data points outside the whisker range. Reported p values are from Mann–Whitney test. e, f DNA-binding analyses of FOXA1 DBD with SNV-containing DNAs. The genomic positions and DNA substrates are indicated at the top of each panel with a representative FOXA1 motif. The position of the SNV is highlighted with light blue boxes. The band intensities were calculated using ImageJ software. Totally, 20 bp double-stranded DNAs were incubated with the FOXA1 DBD. The concentration of FOXA1 DBD was as follows: 0 μM, lanes 1,6; 0.15 μM lanes 2,7; 0.3 μM, lanes 3,8; 0.6 μM, lanes 4,9; 1.2 μM, lanes 5,10. The protein–DNA complex was separated by native-polyacrylamide gel electrophoresis. Browser tracks of ChIP-seq data for each locus is shown below the DNA-binding data