Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome

Michael Bremang, Alessandro Cuomo, Anna Maria Agresta, Magdalena Stugiewicz, Valeria Spadotto, Tiziana Bonaldi

Research output: Contribution to journalArticle

88 Citations (Scopus)

Abstract

Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.

Original languageEnglish
Pages (from-to)2231-2247
Number of pages17
JournalMolecular BioSystems
Volume9
Issue number9
DOIs
Publication statusPublished - 2013

Fingerprint

Proteome
Methylation
Lysine
Arginine
Mass Spectrometry
Isotope Labeling
Proteins
Cell Culture Techniques
Amino Acids
Chromatin Assembly and Disassembly
Post Translational Protein Processing
Proteomics
Histones
Chromatin
Gene Expression

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Medicine(all)

Cite this

Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. / Bremang, Michael; Cuomo, Alessandro; Agresta, Anna Maria; Stugiewicz, Magdalena; Spadotto, Valeria; Bonaldi, Tiziana.

In: Molecular BioSystems, Vol. 9, No. 9, 2013, p. 2231-2247.

Research output: Contribution to journalArticle

Bremang, Michael ; Cuomo, Alessandro ; Agresta, Anna Maria ; Stugiewicz, Magdalena ; Spadotto, Valeria ; Bonaldi, Tiziana. / Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. In: Molecular BioSystems. 2013 ; Vol. 9, No. 9. pp. 2231-2247.
@article{9f6006421dfc40a99fdc4ff628380a8f,
title = "Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome",
abstract = "Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.",
author = "Michael Bremang and Alessandro Cuomo and Agresta, {Anna Maria} and Magdalena Stugiewicz and Valeria Spadotto and Tiziana Bonaldi",
year = "2013",
doi = "10.1039/c3mb00009e",
language = "English",
volume = "9",
pages = "2231--2247",
journal = "Molecular BioSystems",
issn = "1742-206X",
publisher = "Royal Society of Chemistry",
number = "9",

}

TY - JOUR

T1 - Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome

AU - Bremang, Michael

AU - Cuomo, Alessandro

AU - Agresta, Anna Maria

AU - Stugiewicz, Magdalena

AU - Spadotto, Valeria

AU - Bonaldi, Tiziana

PY - 2013

Y1 - 2013

N2 - Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.

AB - Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.

UR - http://www.scopus.com/inward/record.url?scp=84881113123&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84881113123&partnerID=8YFLogxK

U2 - 10.1039/c3mb00009e

DO - 10.1039/c3mb00009e

M3 - Article

C2 - 23748837

AN - SCOPUS:84881113123

VL - 9

SP - 2231

EP - 2247

JO - Molecular BioSystems

JF - Molecular BioSystems

SN - 1742-206X

IS - 9

ER -