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^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

29 Scopus citations

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 (US)
Pages (from-to)	303-308
Number of pages	6
Journal	Nature Methods
Volume	18
Issue number	3
DOIs	https://doi.org/10.1038/s41592-020-01052-9
State	Published - Mar 2021

Funding

ASJC Scopus subject areas

Molecular Biology
Biochemistry
Biotechnology
Cell Biology

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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.",

author = "Schachner, {Luis F.} and Kevin Joo{\ss} and Morgan, {Marc A.} and Andrea Piunti and Meiners, {Matthew J.} and Kafader, {Jared O.} and Lee, {Alexander S.} and Marta Iwanaszko and Cheek, {Marcus A.} and Burg, {Jonathan M.} and Howard, {Sarah A.} and Keogh, {Michael Christopher} and Ali Shilatifard and Kelleher, {Neil L.}",

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2021",

month = mar,

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

language = "English (US)",

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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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Decoding the protein composition of whole nucleosomes with Nuc-MS

Abstract

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