title: Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.
abstract: Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.
authors.affiliation: Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Campus de Luminy, Marseille, France.
authors.forename: Frederic
authors.initials: F
authors.lastname: Koch
authors.forename: Romain
authors.initials: R
authors.lastname: Fenouil
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.forename: Pierre
authors.initials: P
authors.lastname: Cauchy
authors.forename: Thomas K
authors.initials: TK
authors.lastname: Albert
authors.forename: Joaquin
authors.initials: J
authors.lastname: Zacarias-Cabeza
authors.forename: Salvatore
authors.initials: S
authors.lastname: Spicuglia
authors.forename: Albane Lamy
authors.initials: AL
authors.lastname: de la Chapelle
authors.forename: Martin
authors.initials: M
authors.lastname: Heidemann
authors.forename: Corinna
authors.initials: C
authors.lastname: Hintermair
authors.forename: Dirk
authors.initials: D
authors.lastname: Eick
authors.forename: Ivo
authors.initials: I
authors.lastname: Gut
authors.forename: Pierre
authors.initials: P
authors.lastname: Ferrier
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Andrau
mesh_terms: D000818:Animals; D018899:CpG Islands; D004247:DNA / Q000737:chemistry*; D004742:Enhancer Elements, Genetic; D051379:Mice; D026723:Polyadenylation; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000737:chemistry / Q000502:physiology*; D035165:Transcription Factors, General / Q000737:chemistry / Q000378:metabolism* / Q000502:physiology; D024363:Transcription Initiation Site
chemical_list: D035165:Transcription Factors, General; D004247:DNA; D012319:RNA Polymerase II