title: CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters.
abstract: One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties that correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion and show that CpG content and CGI width correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals.
authors.affiliation: Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille University, UM2, Marseille, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Fenouil
authors.forename: Pierre
authors.initials: P
authors.lastname: Cauchy
authors.forename: Frederic
authors.initials: F
authors.lastname: Koch
authors.forename: Nicolas
authors.initials: N
authors.lastname: Descostes
authors.forename: Joaquin Zacarias
authors.initials: JZ
authors.lastname: Cabeza
authors.forename: Charlène
authors.initials: C
authors.lastname: Innocenti
authors.forename: Pierre
authors.initials: P
authors.lastname: Ferrier
authors.forename: Salvatore
authors.initials: S
authors.lastname: Spicuglia
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.forename: Ivo
authors.initials: I
authors.lastname: Gut
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Andrau
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics*; D002478:Cells, Cultured; D042002:Chromatin Assembly and Disassembly; D018899:CpG Islands / Q000235:genetics*; D017353:Gene Deletion; D056726:Genetic Association Studies / Q000379:methods; D008322:Mammals / Q000235:genetics; D051379:Mice; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D016385:TATA Box / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D009707:Nucleosomes; D014157:Transcription Factors