TY - JOUR T1 - Evidence for Gene-Specific Rather Than Transcription Rate–Dependent Histone H3 Exchange in Yeast Coding Regions A1 - Gat-Viks, Irit A1 - Vingron, Martin Y1 - 2009/02/06 N2 - Author Summary During nucleosome disassembly and reassembly, evicted histones are exchanged with newly synthesized histones. Histone exchange occurs in several DNA metabolism processes, including replication, transcription, and repair. Recent reports from several labs show that replication-independent histone H3 exchange in yeast coding regions is tightly correlated with transcription rate. We have computationally shown that histone exchange variability among genes is not only a consequence of transcription rate. Instead, each coding region has a characteristic amount of replication-independent histone exchange, even when excluding the confounding effect of transcription rate. We show that this transcription rate–independent exchange, referred to as relative exchange, is a reproducible and consistent feature of the entire coding region and cannot be explained by regional effects. Next, we characterize the relations between relative exchange and a variety of histone H3 modifications, as well as the histone chaperone Asf1. Taken together, our analysis shows that gene-specific replication-independent histone H3 exchange in coding regions is mediated independently of transcription rate, thus constituting a new mechanism in epigenetic transcription regulation. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 5 IS - 2 UR - https://doi.org/10.1371/journal.pcbi.1000282 SP - e1000282 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000282 ER -