title: Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization.
abstract: Insulators or chromatin boundary elements are defined by their ability to block transcriptional activation by an enhancer and to prevent the spread of active or silenced chromatin. Recent studies have increasingly suggested that insulator proteins play a role in large-scale genome organization. To better understand insulator function on the global scale, we conducted a genome-wide analysis of the binding sites for the insulator protein CTCF in Drosophila by Chromatin Immunoprecipitation (ChIP) followed by a tiling-array analysis. The analysis revealed CTCF binding to many known domain boundaries within the Abd-B gene of the BX-C including previously characterized Fab-8 and MCP insulators, and the Fab-6 region. Based on this finding, we characterized the Fab-6 insulator element. In genome-wide analysis, we found that dCTCF-binding sites are often situated between closely positioned gene promoters, consistent with the role of CTCF as an insulator protein. Importantly, CTCF tends to bind gene promoters just upstream of transcription start sites, in contrast to the predicted binding sites of the insulator protein Su(Hw). These findings suggest that CTCF plays more active roles in regulating gene activity and it functions differently from other insulator proteins in organizing the Drosophila genome.
authors.affiliation: The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.
authors.forename: Sheryl T
authors.initials: ST
authors.lastname: Smith
authors.forename: Priyankara
authors.initials: P
authors.lastname: Wickramasinghe
authors.forename: Andrew
authors.initials: A
authors.lastname: Olson
authors.forename: Dmitri
authors.initials: D
authors.lastname: Loukinov
authors.forename: Lan
authors.initials: L
authors.lastname: Lin
authors.forename: Joy
authors.initials: J
authors.lastname: Deng
authors.forename: Yanping
authors.initials: Y
authors.lastname: Xiong
authors.forename: John
authors.initials: J
authors.lastname: Rux
authors.forename: Ravi
authors.initials: R
authors.lastname: Sachidanandam
authors.forename: Hao
authors.initials: H
authors.lastname: Sun
authors.forename: Victor
authors.initials: V
authors.lastname: Lobanenkov
authors.forename: Jumin
authors.initials: J
authors.lastname: Zhou
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000502:physiology; D004330:Drosophila / Q000196:embryology / Q000235:genetics* / Q000502:physiology; D029721:Drosophila Proteins / Q000235:genetics* / Q000502:physiology; D049750:Genome, Insect; D055106:Genome-Wide Association Study; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000235:genetics* / Q000502:physiology
chemical_list: D000076246:CCCTC-Binding Factor; C524946:CTCF protein, Drosophila; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D012097:Repressor Proteins