GSE98652
Quantitative analysis of the DNA methylation sensitivity of transcription factor complexes
EpiSELEX-seq method was used to characterize the binding preference of human TF complexes to methylated DNA, including BZIP proteins ATF4 and CEBPb, homeodomain TF heterodimers of HM(Meis1)-Pbx1 together with either HoxA1, HoxA5 or HoxA9 and tumor suppressor protein p53. Overall design: One round of EpiSELEX-seq was performed for all TFs tested as described in Kribelbauer et al. Purified TFs were incubated with a mix of methylated and unmethylated randomized 16bp (26bp for p53) DNA libraries of sequence GGTAGTGGAGG-TGGG-CCTGG-16xN/26xN-CCAGG-GAGGTGGAGTAGG for unmethylated and GGTAGTGGAGG-GCAC-CCTGG-16xN/26xN-CCAGG-GAGGTGGAGTAGG for methylated library. Bound fractions were amplified and sequenced.