Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast

Histone exchange between histones carrying position-specific marks and histones bearing general marks is important for gene regulation, but understanding of histone exchange remains incomplete. To overcome the poor time resolution of conventional pulse-chase histone labeling, we present a genetically encoded histone exchange timer sensitive to the duration that two tagged histone subunits co-reside at an individual genomic locus. We apply these sensors to map genome-wide patterns of histone exchange in yeast using single samples. Comparing H3 exchange in cycling and G1-arrested cells suggests that replication-independent H3 exchange occurs at several hundred nucleosomes (<1% of all nucleosomes) per minute, with a maximal rate at histone promoters. We observed substantial differences between the two nucleosome core subcomplexes: H2A-H2B subcomplexes undergo rapid transcription-dependent replacement within coding regions, whereas H3-H4 replacement occurs predominantly within promoter nucleosomes, in association with gene activation or repression. Our timers allow the in vivo study of histone exchange dynamics with minute time scale resolution.

Automated summary

This study introduces a genetically encoded histone exchange timer to monitor the duration that two tagged histone subunits co-reside at an individual genomic locus, allowing for genome-wide mapping of histone exchange patterns using single samples in yeast. The research reveals that H3 exchange predominantly occurs at histone promoters independent of replication, with differences observed in the replacement dynamics between two nucleosome core subcomplexes. This timer offers a minute time scale resolution for studying histone exchange dynamics in vivo.