Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes

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Abstract

Chromatin transactions are typically studied in vivo, or in vitro using artificial chromatin lacking the epigenetic complexity of the natural material. Attempting to bridge the gap between these approaches, we established a system for isolating the yeast genome as a library of mono-nucleosomes harboring the natural epigenetic signature, suitable for biochemical manipulation. Combined with deep sequencing, this library was used to investigate the stability of individual nucleosomes, and - as proof of principle - the nucleosome preference of the chromatin remodeling complex, RSC. This approach uncovered a distinct preference of RSC for nucleosomes derived from regions with a high density of histone variant H2A.Z, and this preference is indeed markedly diminished using nucleosomes from cells lacking H2A.Z. The preference for H2A.Z remodeling/nucleosome ejection can also be reconstituted with recombinant nucleosome arrays. Together, our data indicate that, despite being separated from their genomic context, individual nucleosomes can retain their original identity as promoter- or transcription start site (TSS)-nucleosomes. Besides shedding new light on substrate-preference of the chromatin remodeler RSC, the simple experimental system outlined here should be generally applicable to the study of chromatin transactions.

Journal details

Journal Genome Research
Volume 29
Issue number 6
Pages 988-998
Available online
Publication date

Crick labs/facilities

Acknowledged team

Crick authors

Crick First author
Crick Corresponding author