Open AccessDecoding the protein composition of whole nucleosomes with Nuc-MS
Author(s) -
Luis F. Schachner,
Kevin Jooß,
Marc A. Morgan,
Andrea Piunti,
Matthew J. Meiners,
Jared O. Kafader,
Alexander S. Lee,
Marta Iwanaszko,
Marcus A. Cheek,
Jonathan M. Burg,
Sarah A. Howard,
Michael Christopher Keogh,
Ali Shilatifard,
Neil L. Kelleher
Publication year - 2021
Publication title -
nature methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 19.469
H-Index - 318
eISSN - 1548-7105
pISSN - 1548-7091
DOI - 10.1038/s41592-020-01052-9
Subject(s) - nucleosome , histone , chromatin immunoprecipitation , histone code , immunoprecipitation , biology , chromatin , euchromatin , computational biology , chip on chip , histone h3 , genetics , microbiology and biotechnology , dna , gene , gene expression , heterochromatin , promoter
Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the 'histone code'. To preserve nucleosome-level information, we developed Nuc-MS, which displays the landscape of histone variants and their post-translational modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (sixfold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (for example, a >15-fold enrichment of dimethylated H3K79me2). Nuc-MS is highly concordant with chromatin immunoprecipitation-sequencing (ChIP-seq) and offers a new readout of nucleosome-level biology.