title: Nature and function of insulator protein binding sites in the Drosophila genome.
abstract: Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together, these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes.
authors: Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden. yuri.schwartz@molbiol.umu.se
authors: Yuri B
authors: YB
authors: Schwartz
authors: Daniela
authors: D
authors: Linder-Basso
authors: Peter V
authors: PV
authors: Kharchenko
authors: Michael Y
authors: MY
authors: Tolstorukov
authors: Maria
authors: M
authors: Kim
authors: Hua-Bing
authors: HB
authors: Li
authors: Andrey A
authors: AA
authors: Gorchakov
authors: Aki
authors: A
authors: Minoda
authors: Gregory
authors: G
authors: Shanower
authors: Artyom A
authors: AA
authors: Alekseyenko
authors: Nicole C
authors: NC
authors: Riddle
authors: Youngsook L
authors: YL
authors: Jung
authors: Tingting
authors: T
authors: Gu
authors: Annette
authors: A
authors: Plachetka
authors: Sarah C R
authors: SC
authors: Elgin
authors: Mitzi I
authors: MI
authors: Kuroda
authors: Peter J
authors: PJ
authors: Park
authors: Mikhail
authors: M
authors: Savitsky
authors: Gary H
authors: GH
authors: Karpen
authors: Vincenzo
authors: V
authors: Pirrotta
mesh_terms: D000818:Animals; D001665:Binding Sites; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D049750:Genome, Insect; D006657:Histones / Q000378:metabolism; D038101:Insulator Elements; D008745:Methylation; D008869:Microtubule-Associated Proteins / Q000235:genetics / Q000378:metabolism*; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D063146:Polycomb-Group Proteins / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D034741:RNA, Small Interfering; D014158:Transcription, Genetic
chemical_list: C107964:CP190 protein, Drosophila; D029721:Drosophila Proteins; D006657:Histones; D008869:Microtubule-Associated Proteins; D009687:Nuclear Proteins; D063146:Polycomb-Group Proteins; D034741:RNA, Small Interfering