Partitioned Usage of Chromatin Remodelers by Nucleosome Displacing Factors

Nucleosome-displacing factors (NDFs) in yeast, similar to pioneer factors in higher eukaryotes, cause opening of closed chromatin and formation of nucleosome-depleted regions (NDRs). NDRs in yeast are also affected by ATP-dependent chromatin remodelers (CRs). However, how NDFs and CRs coordinate in nucleosome invasion and NDR formation is still unclear. Here, we designed a high-throughput method to systematically study the interplay between NDFs and CRs. By combining integrated synthetic oligonucleotide library with DNA methyltransferase-based, single-molecule nucleosome mapping, we measured the impact of CRs on NDRs generated by individual NDFs. We found that CRs were dispensable for nucleosome invasion by NDFs, and they function downstream of NDF binding to modulate the NDR length. A few CRs show high specificity towards certain NDFs; however, in most cases, CRs are recruited in a factor-nonspecific and length-dependent manner. Overall, our study represents a novel framework to investigate how NDFs and CRs cooperate to generate desired pattern of chromatin opening. Study of NDR change on synthetic oligo libraries in four remodeler depletion yeast strains and one WT yeast strain. Each sample contains 2-3 replicates.