Nucleosome positioning in A549 cells before/after NME2 induction

Previous studies have analyzed patterns of transcription, transcription factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown. For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF. Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally (in close vicinity of their binding sites) or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy; finally, do all TF binding and associated nucleosome occupancy changes result in altered gene expression? With these in mind, we sought to study a single TF that induces physiological changes, and following characterization of the two states (before and after induction of the TF) we determined: (a) genomic binding sites of the TF, (b) promoter nucleosome occupancy and (c) transcriptome profiles, independently in both conditions. Results demonstrate that TF binding influences expression of the target gene only when it is coupled to nucleosome repositioning at or close to its binding site, and not when transcription factor binding occurs without local associated nucleosome reorganization. The nature of interaction between TF binding and nucleosomes and what extent it influences transcription