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

Gilad YaakovFelix JonasNaama Barkai
Published in: Nature biotechnology (2021)
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.
Keyphrases
  • dna methylation
  • genome wide
  • copy number
  • gene expression
  • transcription factor
  • blood pressure
  • body composition
  • single molecule
  • signaling pathway
  • saccharomyces cerevisiae
  • cell death
  • low cost