Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast
- 8 July 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Biotechnology
- Vol. 39 (11), 1434-1443
- https://doi.org/10.1038/s41587-021-00959-8
Abstract
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.Keywords
This publication has 73 references indexed in Scilit:
- Making sense of transcribing chromatinCurrent Opinion in Cell Biology, 2012
- Regulation of chromatin by histone modificationsCell Research, 2011
- Dynamic changes in histone acetylation regulate origins of DNA replicationNature Structural & Molecular Biology, 2010
- Recombination-induced tag exchange to track old and new proteinsProceedings of the National Academy of Sciences of the United States of America, 2009
- Insights into SAGA function during gene expressionEMBO Reports, 2009
- Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencingProceedings of the National Academy of Sciences of the United States of America, 2009
- The DNA-encoded nucleosome organization of a eukaryotic genomeNature, 2008
- A genomic code for nucleosome positioningNature, 2006
- Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray ProfileCell, 2005
- A versatile toolbox for PCR‐based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettesYeast, 2004