Stability of histone post-translational modifications in samples derived from liver tissue and primary hepatic cells

Philip A. Gruppuso, Joan M. Boylan, Valerie Zabala, Nicola Neretti, Nebiyu A. Abshiru, Jacek W. Sikora, Emma H. Doud, Jeannie M. Camarillo, Paul M. Thomas, Neil L. Kelleher, Jennifer A. Sanders*

*Corresponding author for this work

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Chromatin structure, a key contributor to the regulation of gene expression, is modulated by a broad array of histone post-translational modifications (PTMs). Taken together, these “histone marks” comprise what is often referred to as the “histone code”. The quantitative analysis of histone PTMs by mass spectrometry (MS) offers the ability to examine the response of the histone code to physiological signals. However, few studies have examined the stability of histone PTMs through the process of isolating and culturing primary cells. To address this, we used bottom-up, MS-based analysis of histone PTMs in liver, freshly isolated hepatocytes, and cultured hepatocytes from adult male Fisher F344 rats. Correlations between liver, freshly isolated cells, and primary cultures were generally high, with R2 values exceeding 0.9. However, a number of acetylation marks, including those on H2A K9, H2A1 K13, H3 K4, H3 K14, H4 K8, H4 K12 and H4 K16 differed significantly among the three sources. Inducing proliferation of primary adult hepatocytes in culture affected several marks on histones H3.1/3.2 and H4. We conclude that hepatocyte isolation, culturing and cell cycle status all contribute to steady-state changes in the levels of a number of histone PTMs, indicating changes in histone marks that are rapidly induced in response to alterations in the cellular milieu. This has implications for studies aimed at assigning biological significance to histone modifications in tumors versus cancer cells, the developmental behavior of stem cells, and the attribution of changes in histone PTMs to altered cell metabolism.

Original languageEnglish (US)
Article numbere0203351
JournalPloS one
Volume13
Issue number9
DOIs
StatePublished - Sep 2018

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Gruppuso, P. A., Boylan, J. M., Zabala, V., Neretti, N., Abshiru, N. A., Sikora, J. W., Doud, E. H., Camarillo, J. M., Thomas, P. M., Kelleher, N. L., & Sanders, J. A. (2018). Stability of histone post-translational modifications in samples derived from liver tissue and primary hepatic cells. PloS one, 13(9), [e0203351]. https://doi.org/10.1371/journal.pone.0203351