Complete workflow for analysis of histone post-translational modifications using bottom-up mass spectrometry: From histone extraction to data analysis

Simone Sidoli, Natarajan V. Bhanu, Kelly R. Karch, Xiaoshi Wang, Benjamin A. Garcia

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone function is mediated by extensive post-translational modification by a myriad of nuclear proteins. These modifications are critical for nuclear integrity as they regulate chromatin structure and recruit enzymes involved in gene regulation, DNA repair and chromosome condensation. Even though a large part of the scientific community adopts antibody-based techniques to characterize histone PTM abundance, these approaches are low throughput and biased against hypermodified proteins, as the epitope might be obstructed by nearby modifications. This protocol describes the use of nano liquid chromatography (nLC) and mass spectrometry (MS) for accurate quantification of histone modifications. This method is designed to characterize a large variety of histone PTMs and the relative abundance of several histone variants within single analyses. In this protocol, histones are derivatized with propionic anhydride followed by digestion with trypsin to generate peptides of 5 - 20 aa in length. After digestion, the newly exposed N-termini of the histone peptides are derivatized to improve chromatographic retention during nLC-MS. This method allows for the relative quantification of histone PTMs spanning four orders of magnitude.

Original languageEnglish (US)
Article numbere54112
JournalJournal of Visualized Experiments
Volume2016
Issue number111
DOIs
StatePublished - May 17 2016
Externally publishedYes

Fingerprint

Pulse time modulation
Workflow
Post Translational Protein Processing
Histones
Mass spectrometry
Mass Spectrometry
Liquid chromatography
Peptides
DNA
Proteins
Epitopes
Chromosomes
Gene expression
Antibodies
Condensation
Repair
Enzymes
Throughput
Liquid Chromatography
Chromatin

Keywords

  • Biochemistry
  • Histones
  • Issue 111
  • Liquid chromatography
  • Mass spectrometry
  • Post-translational modifications
  • Propionylation
  • Workflow

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Complete workflow for analysis of histone post-translational modifications using bottom-up mass spectrometry : From histone extraction to data analysis. / Sidoli, Simone; Bhanu, Natarajan V.; Karch, Kelly R.; Wang, Xiaoshi; Garcia, Benjamin A.

In: Journal of Visualized Experiments, Vol. 2016, No. 111, e54112, 17.05.2016.

Research output: Contribution to journalArticle

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