title: Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants.
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.
authors: The Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA 19104 USA.|Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.
authors: Kyoung-Jae
authors: KJ
authors: Won
authors: The Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA 19104 USA.|Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.|Department of Agricultural Biotechnology, National Academy of Agricultural Science, 370 Nongsaengmyeong-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 560-500 South Korea.
authors: Inchan
authors: I
authors: Choi
authors: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.
authors: Gary
authors: G
authors: LeRoy
authors: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.|Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.
authors: Barry M
authors: BM
authors: Zee
authors: Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.
authors: Simone
authors: S
authors: Sidoli
authors: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.|Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.
authors: Michelle
authors: M
authors: Gonzales-Cope
authors: Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.
authors: Benjamin A
authors: BA
authors: Garcia