Intrinsically Disordered Regions Steer the Function Coordination of the Traveling Chromatin Modifier During Pol II Elongation

The Rpd3S histone deacetylase complex suppresses cryptic initiation and maintains genomic integrity by deacetylating transcribed nucleosomes subsequent to RNA Pol II passage. Recent cryo-EM structure analysis of Rpd3S emphasized the significance of two asymmetrical Rco1/Eaf3 dimers in nucleosome binding. However, the mechanism by which Rpd3S interacts with nucleosomal substrates while traveling with elongating Pol II remains elusive. In this study, we elucidate the crucial role of the Rco1 N-terminal Intrinsically Disordered Region (IDR) in regulating Pol II association. Mutations within the K/R cluster of Rco1 IDR significantly impede Rpd3S binding to the C-terminal domain of Rpb1, the largest of subunits of Pol II (CTD), while leaving the overall complex integrity and nucleosome recognition unaffected. Moreover, we identify the Rco1-PHD1 and Eaf3-CHD domains as the minimal module responsible for specific interaction with Ser5-phosphorylated CTD. The Rco1 IDR functions by relieving autoinhibition from its C-terminal regions, thus enabling the binding of PHD1-CHD to CTD. Additionally, we uncover an evolutionarily conserved mechanism governing the distinct roles of the asymmetrical Rco1/Eaf3 dimers in coordinating nucleosome engagement and Pol II binding. These findings offer valuable new perspectives on the functional dynamics of mobile epigenetic modifying complexes that accompany processive machinery.