Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.
Bottom Line: 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 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 and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression?
Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.Show MeSH
Mentions: We next asked whether altered state of chromatin in regulatory regions influenced NME2 occupancy and consequent gene expression changes. To test this, nucleosome positions were determined in the A549 cells before and after NME2 induction. Mono-nucleosomes were isolated by MNase digestion and we mapped nucleosome positions to putative promoter regions (−7.5 kb to 2.5 kb of TSSs) using tiled microarrays (Figure 2A) and found 157 634 and 162 570 nucleosomes before and after NME2 induction, respectively. Next, we checked the relationship between overall number of nucleosomes on each promoter and the expression level of corresponding gene and found that enriched promoter-nucleosome occupancy correlated with decreased expression of corresponding genes (r = −0.73; P < 0.05 before NME2 induction and r = −0.80; P < 0.05 after NME2 induction, Pearson correlation; Figure 2B).
Affiliation: GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India.