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PMID: 17616980 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex.

PLoS genetics ·Vol. 3 ·No. 7 ·2007-07-00 ·Pages e112

Holohan EE, Kwong C, Adryan B, Bartkuhn M, Herold M, Renkawitz R, Russell S, White R

Abstract

Insulator or enhancer-blocking elements are proposed to play an important role in the regulation of transcription by preventing inappropriate enhancer/promoter interaction. The zinc-finger protein CTCF is well studied in vertebrates as an enhancer blocking factor, but Drosophila CTCF has only been characterised recently. To date only one endogenous binding location for CTCF has been identified in the Drosophila genome, the Fab-8 insulator in the Abdominal-B locus in the Bithorax complex (BX-C). We carried out chromatin immunopurification coupled with genomic microarray analysis to identify CTCF binding sites within representative regions of the Drosophila genome, including the 3-Mb Adh region, the BX-C, and the Antennapedia complex. Location of in vivo CTCF binding within these regions enabled us to construct a robust CTCF binding-site consensus sequence. CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8. Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; "Fab-2," "Fab-3," and "Fab-4." With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism. Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.

MeSH Terms
Animals Base Sequence Binding Sites/genetics CCCTC-Binding Factor Chromatin Immunoprecipitation Consensus Sequence DNA/genetics,metabolism DNA Primers/genetics DNA-Binding Proteins/genetics,metabolism Drosophila/genetics,metabolism Drosophila Proteins/genetics,metabolism Enhancer Elements, Genetic Genes, Insect Genome, Insect Insulator Elements Models, Genetic Oligonucleotide Array Sequence Analysis Repressor Proteins/genetics,metabolism
Chemicals
CCCTC-Binding Factor CTCF protein, Drosophila DNA Primers DNA-Binding Proteins Drosophila Proteins Repressor Proteins DNA
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Holohan Eimear E
Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.
Kwong Camilla
Adryan Boris
Bartkuhn Marek
Herold Martin
Renkawitz Rainer
Russell Steven
White Robert
Conflict of Interest

Competing interests. The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.0030112
Published
2007-07-00
Pages
e112
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC1904468
Subset
IM
Grants
Medical Research Council · G8225539 · United Kingdom
Medical Research Council · MC_U105161047 · United Kingdom
Biotechnology and Biological Sciences Research Council · United Kingdom
External Links
PubMed source DOI: 10.1371/journal.pgen.0030112 PMC Full Text View journal details
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