Investigating pioneer factor activity and its coordination with chromatin remodelers using integrated synthetic oligo assay

Chromatin accessibility is regulated by pioneer factors (PFs) and chromatin remodelers (CRs). Here, we present a protocol, based on integrated synthetic oligonucleotide libraries in yeast, to systematically interrogate the nucleosome-displacing activities of PFs and their coordination with CRs. We describe steps for designing oligonucleotide sequences, constructing yeast libraries, measuring nucleosome configurations, and data analyses. This approach potentially can be adapted for use in higher eukaryotes to investigate the activities of many types of chromatin-associated factors. For complete details on the use and execution of this protocol, please refer to Yan et al.,¹ and Chen et al.²