title: Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS.
abstract: Post-translational modifications (PTMs) of histones play a major role in regulating chromatin dynamics and influence processes such as transcription and DNA replication. Here, we report 114 distinct combinations of coexisting PTMs of histone H3 obtained from mouse embryonic stem (ES) cells. Histone H3 N-terminal tail peptides (amino acids 1-50, 5-6 kDa) were separated by optimized weak cation exchange/hydrophilic interaction liquid chromatography (WCX/HILIC) and sequenced online by electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS). High mass accuracy and near complete sequence coverage allowed unambiguous mapping of the major histone marks and discrimination between isobaric and nearly isobaric PTMs such as trimethylation and acetylation. Hierarchical data analysis identified H3K27me2-H3K36me2 as the most frequently observed PTMs in H3. Modifications at H3 residues K27 and K36 often coexist with the abundant mark K23ac, and we identified two frequently occurring quadruplet marks 'K9me1K23acK27me2K36me2' and 'K9me3K23acK27me2K36me', which might indicate a role in crosstalk. Co-occurrence frequency analysis revealed also an interplay between methylations of K9, K27, and K36, suggesting interdependence between histone methylation marks. We hypothesize that the most abundant coexisting PTMs may provide a signature for the permissive state of mouse ES cells.
authors.affiliation: Centre for Epigenetics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Hye Ryung
authors.initials: HR
authors.lastname: Jung
authors.forename: Simone
authors.initials: S
authors.lastname: Sidoli
authors.forename: Simon
authors.initials: S
authors.lastname: Haldbo
authors.forename: Richard R
authors.initials: RR
authors.lastname: Sprenger
authors.forename: Veit
authors.initials: V
authors.lastname: Schwämmle
authors.forename: Diego
authors.initials: D
authors.lastname: Pasini
authors.forename: Kristian
authors.initials: K
authors.lastname: Helin
authors.forename: Ole N
authors.initials: ON
authors.lastname: Jensen
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D053595:Embryonic Stem Cells / Q000737:chemistry* / Q000502:physiology*; D006657:Histones / Q000032:analysis* / Q000235:genetics*; D051379:Mice; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D006657:Histones