RT Journal
A1 Cakiroglu, Aylin
A1 Clapier, Cedric R.
A1 Ehrensberger, Andreas H.
A1 Darbo, Elodie
A1 Cairns, Bradley R.
A1 Luscombe, Nicholas M.
A1 Svejstrup, Jesper Q.
T1 Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes
JF Genome Research 
JO Genome Research 
YR 2019 
FD June 01 
VO 29 
IS 6 
SP 988 
OP 998 
DO 10.1101/gr.243139.118 
UL http://genome.cshlp.org/content/29/6/988.abstract 
AB 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 mononucleosomes 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 H2AZ, and this preference is indeed markedly diminished using nucleosomes from cells lacking H2AZ. The preference for H2AZ 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.