Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection

• DOI: 10.1101/gr.5655606
• Publication Date: 2006-10-20T01:14:40Z
• Authors: Xiao Liu; Cheol-Koo Lee; Joshua A. Granek; Neil D. Clarke; Jason D. Lieb
• Keywords: Linker DNA; DNA binding site; HMG-box; ChIP-sequencing; ChIP-on-chip; genomic DNA

Sequence motifs that are potentially recognized by DNA-binding proteins occur far more often in genomic DNA than do observed vivo protein–DNA interactions. To determine how chromatin influences the utilization of particular sites, we compared genome-wide binding location yeast transcription factor Leu3 to on same absence any protein cofactors. We found DNA-sequence motif vitro and was functionally indistinguishable, but bound different locations under two conditions. Accounting for nucleosome occupancy addition significantly improved prediction interactions vivo, not sites purified vitro. Use histone modification data does further improve predictions, presumably because their effect is already manifest global distribution. Measurements strains differ genotype show low at loci a consequence binding. These results permit quantitation epigenetic influence exerts binding-site selection, provide evidence an instructive, important role determining patterns regulatory targeting genome-wide.