A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response

Huadong Liu, Marek Galka, Eiichiro Mori, Xuguang Liu, Yu fen Lin, Ran Wei, Paula Pittock, Courtney Voss, Gurpreet Dhami, Xing Li, Masaaki Miyaji, Gilles Lajoie, Benjamin Chen, ShawnShun Cheng Li

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

Lysine methylation occurs on both histone and nonhistone proteins. However, our knowledge on the prevalence and function of nonhistone protein methylation is poor. We describe an approach that combines peptide array, bioinformatics, and mass spectrometry to systematically identify lysine methylation sites and map methyllysine-driven protein-protein interactions. Using this approach, we identified a high-confidence and high-resolution interactome of the heterochromatin protein 1β (HP1β) and uncovered, simultaneously, numerous methyllysine sites on nonhistone proteins. We found that HP1β binds to DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and regulates its localization to double-strand breaks (DSBs) during DNA damage response (DDR). Mutation of the methylation sites in DNA-PKcs or depletion of HP1β in cells caused defects in DDR. Furthermore, we showed that the methylation of DNA-PKcs and many other proteins in the HP1β interactome undergoes large changes in response to DNA damage, indicating that Lys methylation is a highly dynamic posttranslational modification.

Original languageEnglish (US)
Pages (from-to)723-735
Number of pages13
JournalMolecular Cell
Volume50
Issue number5
DOIs
StatePublished - Jun 6 2013

Fingerprint

Methylation
Lysine
DNA Damage
DNA-Activated Protein Kinase
Catalytic Domain
Proteins
Post Translational Protein Processing
Computational Biology
Histones
heterochromatin-specific nonhistone chromosomal protein HP-1
Mass Spectrometry
Peptides
Mutation

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response. / Liu, Huadong; Galka, Marek; Mori, Eiichiro; Liu, Xuguang; Lin, Yu fen; Wei, Ran; Pittock, Paula; Voss, Courtney; Dhami, Gurpreet; Li, Xing; Miyaji, Masaaki; Lajoie, Gilles; Chen, Benjamin; Li, ShawnShun Cheng.

In: Molecular Cell, Vol. 50, No. 5, 06.06.2013, p. 723-735.

Research output: Contribution to journalArticle

Liu, H, Galka, M, Mori, E, Liu, X, Lin, YF, Wei, R, Pittock, P, Voss, C, Dhami, G, Li, X, Miyaji, M, Lajoie, G, Chen, B & Li, SC 2013, 'A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response', Molecular Cell, vol. 50, no. 5, pp. 723-735. https://doi.org/10.1016/j.molcel.2013.04.025
Liu, Huadong ; Galka, Marek ; Mori, Eiichiro ; Liu, Xuguang ; Lin, Yu fen ; Wei, Ran ; Pittock, Paula ; Voss, Courtney ; Dhami, Gurpreet ; Li, Xing ; Miyaji, Masaaki ; Lajoie, Gilles ; Chen, Benjamin ; Li, ShawnShun Cheng. / A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response. In: Molecular Cell. 2013 ; Vol. 50, No. 5. pp. 723-735.
@article{b0325c2c7d7245a99d1e52270efb4439,
title = "A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response",
abstract = "Lysine methylation occurs on both histone and nonhistone proteins. However, our knowledge on the prevalence and function of nonhistone protein methylation is poor. We describe an approach that combines peptide array, bioinformatics, and mass spectrometry to systematically identify lysine methylation sites and map methyllysine-driven protein-protein interactions. Using this approach, we identified a high-confidence and high-resolution interactome of the heterochromatin protein 1β (HP1β) and uncovered, simultaneously, numerous methyllysine sites on nonhistone proteins. We found that HP1β binds to DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and regulates its localization to double-strand breaks (DSBs) during DNA damage response (DDR). Mutation of the methylation sites in DNA-PKcs or depletion of HP1β in cells caused defects in DDR. Furthermore, we showed that the methylation of DNA-PKcs and many other proteins in the HP1β interactome undergoes large changes in response to DNA damage, indicating that Lys methylation is a highly dynamic posttranslational modification.",
author = "Huadong Liu and Marek Galka and Eiichiro Mori and Xuguang Liu and Lin, {Yu fen} and Ran Wei and Paula Pittock and Courtney Voss and Gurpreet Dhami and Xing Li and Masaaki Miyaji and Gilles Lajoie and Benjamin Chen and Li, {ShawnShun Cheng}",
year = "2013",
month = "6",
day = "6",
doi = "10.1016/j.molcel.2013.04.025",
language = "English (US)",
volume = "50",
pages = "723--735",
journal = "Molecular Cell",
issn = "1097-2765",
publisher = "Cell Press",
number = "5",

}

TY - JOUR

T1 - A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response

AU - Liu, Huadong

AU - Galka, Marek

AU - Mori, Eiichiro

AU - Liu, Xuguang

AU - Lin, Yu fen

AU - Wei, Ran

AU - Pittock, Paula

AU - Voss, Courtney

AU - Dhami, Gurpreet

AU - Li, Xing

AU - Miyaji, Masaaki

AU - Lajoie, Gilles

AU - Chen, Benjamin

AU - Li, ShawnShun Cheng

PY - 2013/6/6

Y1 - 2013/6/6

N2 - Lysine methylation occurs on both histone and nonhistone proteins. However, our knowledge on the prevalence and function of nonhistone protein methylation is poor. We describe an approach that combines peptide array, bioinformatics, and mass spectrometry to systematically identify lysine methylation sites and map methyllysine-driven protein-protein interactions. Using this approach, we identified a high-confidence and high-resolution interactome of the heterochromatin protein 1β (HP1β) and uncovered, simultaneously, numerous methyllysine sites on nonhistone proteins. We found that HP1β binds to DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and regulates its localization to double-strand breaks (DSBs) during DNA damage response (DDR). Mutation of the methylation sites in DNA-PKcs or depletion of HP1β in cells caused defects in DDR. Furthermore, we showed that the methylation of DNA-PKcs and many other proteins in the HP1β interactome undergoes large changes in response to DNA damage, indicating that Lys methylation is a highly dynamic posttranslational modification.

AB - Lysine methylation occurs on both histone and nonhistone proteins. However, our knowledge on the prevalence and function of nonhistone protein methylation is poor. We describe an approach that combines peptide array, bioinformatics, and mass spectrometry to systematically identify lysine methylation sites and map methyllysine-driven protein-protein interactions. Using this approach, we identified a high-confidence and high-resolution interactome of the heterochromatin protein 1β (HP1β) and uncovered, simultaneously, numerous methyllysine sites on nonhistone proteins. We found that HP1β binds to DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and regulates its localization to double-strand breaks (DSBs) during DNA damage response (DDR). Mutation of the methylation sites in DNA-PKcs or depletion of HP1β in cells caused defects in DDR. Furthermore, we showed that the methylation of DNA-PKcs and many other proteins in the HP1β interactome undergoes large changes in response to DNA damage, indicating that Lys methylation is a highly dynamic posttranslational modification.

UR - http://www.scopus.com/inward/record.url?scp=84878825857&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84878825857&partnerID=8YFLogxK

U2 - 10.1016/j.molcel.2013.04.025

DO - 10.1016/j.molcel.2013.04.025

M3 - Article

VL - 50

SP - 723

EP - 735

JO - Molecular Cell

JF - Molecular Cell

SN - 1097-2765

IS - 5

ER -