title: Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome.
abstract: Recognition of histone marks by reader modules is thought to be at the heart of epigenetic mechanisms. These protein domains are considered to function by targeting regulators to chromosomal loci carrying specific histone modifications. This is important for proper gene regulation as well as propagation of epigenetic information. The NuA4 acetyltransferase complex contains two of these reader modules, an H3K4me3-specific plant homeodomain (PHD) within the Yng2 subunit and an H3K36me2/3-specific chromodomain in the Eaf3 subunit. While each domain showed a close functional interaction with the respective histone mark that it recognizes, at the biochemical level, genetic level (as assessed with epistatic miniarray profile screens), and phenotypic level, cells with the combined loss of both readers showed greatly enhanced phenotypes. Chromatin immunoprecipitation coupled with next-generation sequencing experiments demonstrated that the Yng2 PHD specifically directs H4 acetylation near the transcription start site of highly expressed genes, while Eaf3 is important downstream on the body of the genes. Strikingly, the recruitment of the NuA4 complex to these loci was not significantly affected. Furthermore, RNA polymerase II occupancy was decreased only under conditions where both PHD and chromodomains were lost, generally in the second half of the gene coding regions. Altogether, these results argue that methylated histone reader modules in NuA4 are not responsible for its recruitment to the promoter or coding regions but, rather, are required to orient its acetyltransferase catalytic site to the methylated histone 3-bearing nucleosomes in the surrounding chromatin, cooperating to allow proper transition from transcription initiation to elongation.
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada.
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Steunou
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada.
authors.forename: Myriam
authors.initials: M
authors.lastname: Cramet
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada.
authors.forename: Dorine
authors.initials: D
authors.lastname: Rossetto
authors.affiliation: Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Aristizabal
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Lacoste
authors.affiliation: Chromatin and Genomic Expression Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada.
authors.forename: Simon
authors.initials: S
authors.lastname: Drouin
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada.
authors.forename: Valérie
authors.initials: V
authors.lastname: Côté
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Paquet
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada.
authors.forename: Rhea T
authors.initials: RT
authors.lastname: Utley
authors.affiliation: Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA.
authors.forename: Nevan
authors.initials: N
authors.lastname: Krogan
authors.affiliation: Chromatin and Genomic Expression Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada.|Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.
authors.forename: François
authors.initials: F
authors.lastname: Robert
authors.affiliation: Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Kobor
authors.affiliation: St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Québec City, Quebec, Canada Jacques.Cote@crhdq.ulaval.ca.
authors.forename: Jacques
authors.identifier: http://orcid.org/0000-0001-6751-555X
authors.initials: J
authors.lastname: Côté
mesh_terms: D000107:Acetylation; D000123:Acetyltransferases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D047369:Chromatin Immunoprecipitation; D044127:Epigenesis, Genetic; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D051548:Histone Acetyltransferases / Q000737:chemistry / Q000378:metabolism*; D042421:Histone Code; D006657:Histones / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site
chemical_list: D006657:Histones; D029701:Saccharomyces cerevisiae Proteins; D000123:Acetyltransferases; C428131:Eaf3 protein, S cerevisiae; C469780:Yng2 protein, S cerevisiae; D051548:Histone Acetyltransferases; C504740:NuA4 protein, S cerevisiae; D012319:RNA Polymerase II