Decoding the protein composition of whole nucleosomes with Nuc-MS

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

doi:10.1038/s41592-020-01052-9

Decoding the protein composition of whole nucleosomes with Nuc-MS

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

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

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.

Original language	English
Pages (from-to)	303-308
Journal	Nature Methods
Volume	18
Issue number	3
DOIs	https://doi.org/10.1038/s41592-020-01052-9
Publication status	Published - 1 Mar 2021
Externally published	Yes

Funding

This work was supported by the National Institute of General Medical Sciences (P41 GM108569) for the National Resource for Translational and Developmental Proteomics at Northwestern University and NIH grants S10OD025194 and RF1AG063903 (Kelleher laboratory) and R44GM116584, R44CA212733 and R44CA214076 (EpiCypher). L.F.S. is a Gilliam Fellow of the Howard Hughes Medical Institute. Research in this publication is also supported by Thermo Fisher Scientific and a fellowship associated with the Chemistry of Life Processes Predoctoral Training grant T32GM105538 at Northwestern University. A.P. is supported by the Transition to Independence grant K99CA234434-01. We also thank M. Senko, P. Compton, C. Koo, L. Szymczak and M. McAnnally for technical assistance and S. Judge and A. Rosenzweig for providing thoughtful suggestions to improve the manuscript.

Funders	Funder number
Northwestern University
National Institutes of Health
NIH Office of the Director	S10OD025194
National Institute of General Medical Sciences	P41GM108569, T32GM105538, R44GM116584
National Cancer Institute	R44CA212733, R44CA214076, K99CA234434
National Institute on Aging	RF1AG063903
Howard Hughes Medical Institute	59008810

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 6 Clean Water and Sanitation

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10.1038/s41592-020-01052-9

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title = "Decoding the protein composition of whole nucleosomes with Nuc-MS",

abstract = "Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the {\textquoteleft}histone code{\textquoteright}. 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.",

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doi = "10.1038/s41592-020-01052-9",

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AU - Schachner, Luis F.

AU - Jooß, Kevin

AU - Morgan, Marc A.

AU - Piunti, Andrea

AU - Meiners, Matthew J.

AU - Kafader, Jared O.

AU - Lee, Alexander S.

AU - Iwanaszko, Marta

AU - Cheek, Marcus A.

AU - Burg, Jonathan M.

AU - Howard, Sarah A.

AU - Keogh, Michael-Christopher

AU - Shilatifard, Ali

AU - Kelleher, Neil L.

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AB - 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.

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JO - Nature Methods

JF - Nature Methods

IS - 3

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Decoding the protein composition of whole nucleosomes with Nuc-MS

Abstract

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UN SDGs

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