title: Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells.
abstract: BACKGROUND
  Pluripotent cells can be differentiated into many different cell types in vitro. Successful differentiation is guided in large part by epigenetic reprogramming and regulation of critical gene expression patterns. Recent genome-wide studies have identified the distribution of different histone-post-translational modifications (PTMs) in various conditions and during cellular differentiation. However, our understanding of the abundance of histone PTMs and their regulatory mechanisms still remain unknown.
  
  
  RESULTS
  Here, we present a quantitative and comprehensive study of the abundance levels of histone PTMs during the differentiation of mouse embryonic stem cells (ESCs) using mass spectrometry (MS). We observed dynamic changes of histone PTMs including increased H3K9 methylation levels in agreement with previously reported results. More importantly, we found a global decrease of multiply acetylated histone H4 peptides. Brd4 targets acetylated H4 with a strong affinity to multiply modified H4 acetylation sites. We observed that the protein levels of Brd4 decreased upon differentiation together with global histone H4 acetylation. Inhibition of Brd4:histone H4 interaction by the BET domain inhibitor (+)-JQ1 in ESCs results in enhanced differentiation to the endodermal lineage, by disrupting the protein abundance dynamics. Genome-wide ChIP-seq mapping showed that Brd4 and H4 acetylation are co-occupied in the genome, upstream of core pluripotency genes such as Oct4 and Nanog in ESCs and lineage-specific genes in embryoid bodies (EBs).
  
  
  CONCLUSIONS
  Together, our data demonstrate the fundamental role of Brd4 in monitoring cell differentiation through its interaction with acetylated histone marks and disruption of Brd4 may cause aberrant differentiation.
authors: Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. micgonzales@gmail.com.
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. sidoli@mail.med.upenn.edu.
authors: Simone
authors: S
authors: Sidoli
authors: Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. nbhanu@mail.med.upenn.edu.
authors: Natarajan V
authors: NV
authors: Bhanu
authors: The Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA, 19104, USA. wonk@mail.med.upenn.edu.|Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. wonk@mail.med.upenn.edu.
authors: Kyoung-Jae
authors: KJ
authors: Won
authors: Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. bgarci@mail.med.upenn.edu.
authors: Benjamin A
authors: BA
authors: Garcia
mesh_terms: D000107:Acetylation; D000818:Animals; D001665:Binding Sites; D002454:Cell Differentiation / Q000187:drug effects; D000066673:Cell Self Renewal / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D016000:Cluster Analysis; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism*; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism*; D051379:Mice; D009687:Nuclear Proteins / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D014212:Tretinoin / Q000494:pharmacology; D000092468:Bromodomain Containing Proteins
chemical_list: D006657:Histones; D009687:Nuclear Proteins; D014157:Transcription Factors; D014212:Tretinoin; C486694:Brd4 protein, mouse; D000092468:Bromodomain Containing Proteins