Analysis of histones in xenopus Laevis II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4

Joshua J. Nicklay, David Shechter, Raghu K. Chitta, Benjamin A. Garcia, Jeffrey Shabanowitz, C. David Allis, Donald F. Hunt

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Epigenetic information is hypothesized to be encoded in his-tone variants and post-translational modifications. Varied cell-and locus-specific combinations of these epigenetic marks are likely contributors to regulation of chromatin-templated transactions, including transcription, replication, recombination, and repair. Therefore, the relative abundance of histone modifications in a given cell type is a potential index of cell fate and specificity. Here, we utilize mass spectrometry techniques to characterize the relative abundance index of cell type-specific modifications on histones H3 and H4 in distinct cell types from the frog Xenopus laevis, including the sperm, the stored prede-position histones in the egg, the early embryo equivalent pronu-clei, cultured somatic cells, and erythrocytes. We used collision-ally associated dissociation to identify the modifications present on histone H3 in a variety of cell types, resolving 26 distinctly modified H3 peptides. We employed the electron transfer dissociation fragmentation technique in a "middle-down" approach on the H4 N-terminal tail to explore the overlap of post-translational modifications. We observed 66 discrete iso-forms of the H4 1-23 fragment in four different cell types. Isolation of the stored, predeposition histone H4 from the frog egg also revealed a more varied pattern of modifications than the previously known diacetylation on Lys 5 and Lys 12. The developmental transitions of modifications on H3 and H4 were strikingly varied, implying a strong correlation of the histone code with cell type and fate. Our results are consistent with a histone code index for each cell type and uncover potential cross-talk between modifications on a single tail.

Original languageEnglish (US)
Pages (from-to)1075-1085
Number of pages11
JournalJournal of Biological Chemistry
Volume284
Issue number2
DOIs
StatePublished - Jan 9 2009
Externally publishedYes

Fingerprint

Xenopus laevis
Histones
Mass spectrometry
Mass Spectrometry
Histone Code
Post Translational Protein Processing
Epigenomics
Anura
Ovum
Tail
Recombinational DNA Repair
Transcription
Chromatin
Repair
Spermatozoa
Cultured Cells
Embryonic Structures
Erythrocytes
Electrons
Peptides

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Analysis of histones in xenopus Laevis II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4. / Nicklay, Joshua J.; Shechter, David; Chitta, Raghu K.; Garcia, Benjamin A.; Shabanowitz, Jeffrey; Allis, C. David; Hunt, Donald F.

In: Journal of Biological Chemistry, Vol. 284, No. 2, 09.01.2009, p. 1075-1085.

Research output: Contribution to journalArticle

Nicklay, Joshua J. ; Shechter, David ; Chitta, Raghu K. ; Garcia, Benjamin A. ; Shabanowitz, Jeffrey ; Allis, C. David ; Hunt, Donald F. / Analysis of histones in xenopus Laevis II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4. In: Journal of Biological Chemistry. 2009 ; Vol. 284, No. 2. pp. 1075-1085.
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