title: RNF40 regulates gene expression in an epigenetic context-dependent manner.
abstract: Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes.
  
  
  
  Using conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss. Furthermore, we find that decreased expression of RNF40-dependent genes is highly associated with widespread narrowing of H3K4me3 peaks. H2Bub1 promotes the broadening of H3K4me3 to increase transcriptional elongation, which together lead to increased tissue-specific gene transcription. Notably, genes upregulated following Rnf40 deletion, including Foxl2, are enriched for H3K27me3, which is decreased following Rnf40 deletion due to decreased expression of the Ezh2 gene. As a consequence, increased expression of some RNF40-"suppressed" genes is associated with enhancer activation via FOXL2.
  
  
  
  Together these findings reveal the complexity and context-dependency whereby one histone modification can have divergent effects on gene transcription. Furthermore, we show that these effects are dependent upon the activity of other epigenetic regulatory proteins and histone modifications.
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
authors.forename: Wanhua
authors.initials: W
authors.lastname: Xie
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
authors.forename: Sankari
authors.initials: S
authors.lastname: Nagarajan
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Baumgart
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
authors.forename: Robyn Laura
authors.initials: RL
authors.lastname: Kosinsky
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
authors.forename: Zeynab
authors.initials: Z
authors.lastname: Najafova
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
authors.forename: Vijayalakshmi
authors.initials: V
authors.lastname: Kari
authors.affiliation: Research Group for Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Griesebachstraße 5, 37077, Göttingen, Germany.
authors.forename: Magali
authors.initials: M
authors.lastname: Hennion
authors.affiliation: Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany.
authors.forename: Daniela
authors.initials: D
authors.lastname: Indenbirken
authors.affiliation: Research Group for Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Griesebachstraße 5, 37077, Göttingen, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bonn
authors.affiliation: Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany.
authors.forename: Adam
authors.initials: A
authors.lastname: Grundhoff
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Wegwitz
authors.affiliation: Department of Molecular Cell Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg, 37077, Göttingen, Germany.|Department of Clinical Neurophysiology, University of Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Mansouri
authors.affiliation: Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. steven.johnsen@med.uni-goettingen.de.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Johnsen
mesh_terms: D000818:Animals; D042863:Cyclin-Dependent Kinase 9 / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D000071221:Enhancer of Zeste Homolog 2 Protein / Q000235:genetics; D044127:Epigenesis, Genetic; D005347:Fibroblasts / Q000378:metabolism; D005786:Gene Expression Regulation; D005801:Genes, Homeobox; D006657:Histones / Q000378:metabolism; D051379:Mice; D018345:Mice, Knockout; D009928:Organ Specificity / Q000235:genetics; D011485:Protein Binding; D061805:Transcription Elongation, Genetic; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D044767:Ubiquitin-Protein Ligases / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D006657:Histones; D000071221:Enhancer of Zeste Homolog 2 Protein; C498410:Ezh2 protein, mouse; C571257:RNF20 protein, mouse; D044767:Ubiquitin-Protein Ligases; D042863:Cyclin-Dependent Kinase 9
keywords: Broad H3K4me3; Enhancer; Epigenetics; Ezh2; FOXL2; H2Bub1; RNF40