title: A wave of nascent transcription on activated human genes.
abstract: Genome-wide studies reveal that transcription by RNA polymerase II (Pol II) is dynamically regulated. To obtain a comprehensive view of a single transcription cycle, we switched on transcription of five long human genes (>100 kbp) with tumor necrosis factor-alpha (TNFalpha) and monitored (using microarrays, RNA fluorescence in situ hybridization, and chromatin immunoprecipitation) the appearance of nascent RNA, changes in binding of Pol II and two insulators (the cohesin subunit RAD21 and the CCCTC-binding factor CTCF), and modifications of histone H3. Activation triggers a wave of transcription that sweeps along the genes at approximately 3.1 kbp/min; splicing occurs cotranscriptionally, a major checkpoint acts several kilobases downstream of the transcription start site to regulate polymerase transit, and Pol II tends to stall at cohesin/CTCF binding sites.
authors.affiliation: Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
authors.forename: Youichiro
authors.initials: Y
authors.lastname: Wada
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Ohta
authors.forename: Meng
authors.initials: M
authors.lastname: Xu
authors.forename: Shuichi
authors.initials: S
authors.lastname: Tsutsumi
authors.forename: Takashi
authors.initials: T
authors.lastname: Minami
authors.forename: Kenji
authors.initials: K
authors.lastname: Inoue
authors.forename: Daisuke
authors.initials: D
authors.lastname: Komura
authors.forename: Jun'ichi
authors.initials: J
authors.lastname: Kitakami
authors.forename: Nobuhiko
authors.initials: N
authors.lastname: Oshida
authors.forename: Argyris
authors.initials: A
authors.lastname: Papantonis
authors.forename: Akashi
authors.initials: A
authors.lastname: Izumi
authors.forename: Mika
authors.initials: M
authors.lastname: Kobayashi
authors.forename: Hiroko
authors.initials: H
authors.lastname: Meguro
authors.forename: Yasuharu
authors.initials: Y
authors.lastname: Kanki
authors.forename: Imari
authors.initials: I
authors.lastname: Mimura
authors.forename: Kazuki
authors.initials: K
authors.lastname: Yamamoto
authors.forename: Chikage
authors.initials: C
authors.lastname: Mataki
authors.forename: Takao
authors.initials: T
authors.lastname: Hamakubo
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Shirahige
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Aburatani
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kimura
authors.forename: Tatsuhiko
authors.initials: T
authors.lastname: Kodama
authors.forename: Peter R
authors.initials: PR
authors.lastname: Cook
authors.forename: Sigeo
authors.initials: S
authors.lastname: Ihara
mesh_terms: D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins; D006801:Humans; D017403:In Situ Hybridization; D007438:Introns; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism; D012326:RNA Splicing; D012333:RNA, Messenger / Q000096:biosynthesis; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics; D000097722:Cohesins
chemical_list: D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D010750:Phosphoproteins; D012319:RNA Polymerase II; D012333:RNA, Messenger; D012097:Repressor Proteins; D014409:Tumor Necrosis Factor-alpha; D000097722:Cohesins; C000619697:CTCF protein, human; C429022:RAD21 protein, human