Nucleosome conformation dictates the histone code

Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized “codes” that are read by specialized domains (reader domains) in chromatin associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP - histone PTM] specificity, and in doing so to decipher the histone code. However, this has largely been done using a reductive approach of isolated reader domains and histone peptides, with the assumption that PTM readout is unaffected by any higher order considerations. Here we show that histone PTM specificity is in fact dependent on nucleosomal context, necessitating we re-define the 'histone code' concept and further interrogate it at the nucleosomal level. Overall design: We performed CUT&RUN for one NURF complex protein, three Histone PTMs, and one IgG control for paired-end sequencing.