title: Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells.
abstract: Epigenetic regulation through chromatin is thought to play a critical role in the establishment and maintenance of pluripotency. Traditionally, antibody-based technologies were used to probe for specific posttranslational modifications (PTMs) present on histone tails, but these methods do not generally reveal the presence of multiple modifications on a single-histone tail (combinatorial codes). Here, we describe technology for the discovery and quantification of histone combinatorial codes that is based on chromatography and mass spectrometry. We applied this methodology to decipher 74 discrete combinatorial codes on the tail of histone H4 from human embryonic stem (ES) cells. Finally, we quantified the abundances of these codes as human ES cells undergo differentiation to reveal striking changes in methylation and acetylation patterns. For example, H4R3 methylation was observed only in the presence of H4K20 dimethylation; such context-specific patterning exemplifies the power of this technique.
authors.affiliation: Department of Chemistry, Integrated Program in Biochemistry, Genome Center of Wisconsin, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Doug
authors.initials: D
authors.lastname: Phanstiel
authors.forename: Justin
authors.initials: J
authors.lastname: Brumbaugh
authors.forename: W Travis
authors.initials: WT
authors.lastname: Berggren
authors.forename: Kevin
authors.initials: K
authors.lastname: Conard
authors.forename: Xuezhu
authors.initials: X
authors.lastname: Feng
authors.forename: Mark E
authors.initials: ME
authors.lastname: Levenstein
authors.forename: Graeme C
authors.initials: GC
authors.lastname: McAlister
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
mesh_terms: D000595:Amino Acid Sequence; D002454:Cell Differentiation; D002460:Cell Line; D053595:Embryonic Stem Cells / Q000737:chemistry* / Q000166:cytology* / Q000378:metabolism; D006657:Histones; D006801:Humans; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D020033:Protein Isoforms / Q000737:chemistry / Q000378:metabolism
chemical_list: D006657:Histones; D020033:Protein Isoforms