Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants

Kyoung Jae Won, Inchan Choi, Gary Leroy, Barry M. Zee, Simone Sidoli, Michelle Gonzales-Cope, Benjamin A. Garcia

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Background: Histone variants play further important roles in DNA packaging and controlling gene expression. However, our understanding about their composition and their functions is limited. Results: Integrating proteomic and genomic approaches, we performed a comprehensive analysis of the epigenetic landscapes containing the four histone variants H3.1, H3.3, H2A.Z, and macroH2A. These histones were FLAG-tagged in HeLa cells and purified using chromatin immunoprecipitation (ChIP). By adopting ChIP followed by mass spectrometry (ChIP-MS), we quantified histone post-translational modifications (PTMs) and histone variant nucleosomal ratios in highly purified mononucleosomes. Subsequent ChIP followed by next-generation sequencing (ChIP-seq) was used to map the genome-wide localization of the analyzed histone variants and define their chromatin domains. Finally, we included in our study large datasets contained in the ENCODE database. We newly identified a group of regulatory regions enriched in H3.1 and the histone variant associated with repressive marks macroH2A. Systematic analysis identified both symmetric and asymmetric patterns of histone variant occupancies at intergenic regulatory regions. Strikingly, these directional patterns were associated with RNA polymerase II (PolII). These asymmetric patterns correlated with the enhancer activities measured using global run-on sequencing (GRO-seq) data. Conclusions: Our studies show that H2A.Z and H3.3 delineate the orientation of transcription at enhancers as observed at promoters. We also showed that enhancers with skewed histone variant patterns well facilitate enhancer activity. Collectively, our study indicates that histone variants are deposited at regulatory regions to assist gene regulation.

Original languageEnglish (US)
Article number13
JournalEpigenetics and Chromatin
Volume8
Issue number1
DOIs
StatePublished - Apr 10 2015
Externally publishedYes

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Nucleic Acid Regulatory Sequences
Histones
Chromatin Immunoprecipitation
Proteogenomics
DNA Packaging
Intergenic DNA
RNA Polymerase II
Post Translational Protein Processing
HeLa Cells
Epigenomics
Proteomics
Chromatin
Mass Spectrometry
Genome
Databases
Gene Expression

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. / Won, Kyoung Jae; Choi, Inchan; Leroy, Gary; Zee, Barry M.; Sidoli, Simone; Gonzales-Cope, Michelle; Garcia, Benjamin A.

In: Epigenetics and Chromatin, Vol. 8, No. 1, 13, 10.04.2015.

Research output: Contribution to journalArticle

Won, Kyoung Jae ; Choi, Inchan ; Leroy, Gary ; Zee, Barry M. ; Sidoli, Simone ; Gonzales-Cope, Michelle ; Garcia, Benjamin A. / Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. In: Epigenetics and Chromatin. 2015 ; Vol. 8, No. 1.
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