title: RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.
abstract: It is widely assumed that the key rate-limiting step in gene activation is the recruitment of RNA polymerase II (Pol II) to the core promoter. Although there are well-documented examples in which Pol II is recruited to a gene but stalls, a general role for Pol II stalling in development has not been established. We have carried out comprehensive Pol II chromatin immunoprecipitation microarray (ChIP-chip) assays in Drosophila embryos and identified three distinct Pol II binding behaviors: active (uniform binding across the entire transcription unit), no binding, and stalled (binding at the transcription start site). The notable feature of the approximately 10% genes that are stalled is that they are highly enriched for developmental control genes, which are either repressed or poised for activation during later stages of embryogenesis. We propose that Pol II stalling facilitates rapid temporal and spatial changes in gene activity during development.
authors.affiliation: Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Julia
authors.initials: J
authors.lastname: Zeitlinger
authors.forename: Alexander
authors.initials: A
authors.lastname: Stark
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Joung-Woo
authors.initials: JW
authors.lastname: Hong
authors.forename: Sergei
authors.initials: S
authors.lastname: Nechaev
authors.forename: Karen
authors.initials: K
authors.lastname: Adelman
authors.forename: Michael
authors.initials: M
authors.lastname: Levine
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
mesh_terms: D000818:Animals; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D004625:Embryo, Nonmammalian; D005786:Gene Expression Regulation; D050437:Genes, Developmental; D049750:Genome, Insect; D015533:Transcriptional Activation
chemical_list: D012321:DNA-Directed RNA Polymerases