title: Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.
abstract: RNA Polymerase II (Pol II) is bound to the promoter regions of many or most developmental control genes before their activation during Drosophila embryogenesis. It has been suggested that Pol II stalling is used to produce dynamic and rapid responses of developmental patterning genes to transient cues such as extracellular signaling molecules. Here, we present a combined computational and experimental analysis of stalled promoters to determine how they come to bind Pol II in the early Drosophila embryo. At least one-fourth of the stalled promoters contain a shared sequence motif, the "pause button" (PB): KCGRWCG. The PB motif is sometimes located in the position of the DPE, and over one-fifth of the stalled promoters contain the following arrangement of core elements: GAGA, Inr, PB, and/or DPE. This arrangement was used to identify additional stalled promoters in the Drosophila genome, and permanganate footprint assays were used to confirm that the segmentation gene engrailed contains paused Pol II as seen for heat-shock genes. We discuss different models for Pol II binding and gene activation in the early embryo.
authors.affiliation: Department Molecular and Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Hendrix
authors.forename: Joung-Woo
authors.initials: JW
authors.lastname: Hong
authors.forename: Julia
authors.initials: J
authors.lastname: Zeitlinger
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
authors.forename: Michael S
authors.initials: MS
authors.lastname: Levine
mesh_terms: D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000378:metabolism; D029721:Drosophila Proteins / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000196:embryology* / Q000201:enzymology / Q000235:genetics; D004625:Embryo, Nonmammalian / Q000201:enzymology; D018507:Gene Expression Regulation, Developmental; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism; D015533:Transcriptional Activation
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D014157:Transcription Factors; C063460:Trl protein, Drosophila; D012319:RNA Polymerase II