The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo

We addressed the roles of three nucleosome spacing enzymes (ISW1, ISW2 and CHD1) in specifying chromatin organization in S. cerevisiae. Overall design: Comparison of budding yeast nucleosome positions obtained using micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq). We sequenced nucleosomes from isogenic strains with the isw1?, isw2? or chd1? mutations in all combinations. We measured gene activity by ChIP-seq for the Rpb3 subunit of RNA polymerase II for some of these mutants.