Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China; National Library of Medicine, National Institutes of Health, Bethesda, United States
Wei Song
National Library of Medicine, National Institutes of Health, Bethesda, United States
Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Canada; Department of Biology and Molecular Sciences, Queen’s University, Kingston, Canada; School of Computing, Queen’s University, Kingston, Canada; Ontario Institute of Cancer Research, Toronto, Canada
Wrapping of DNA into nucleosomes restricts accessibility to DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, initiate local chromatin opening, and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding, and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq, and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2, and HeLa-S3 cell lines. Last, we systematically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.
