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Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila

Boris Adryan12, Gertrud Woerfel1, Ian Birch-Machin1, Shan Gao3, Marie Quick1, Lisa Meadows3, Steven Russell3 and Robert White1*

Author Affiliations

1 Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK

2 Theoretical and Computational Biology Group, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK

3 Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK

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Genome Biology 2007, 8:R167  doi:10.1186/gb-2007-8-8-r167

Published: 16 August 2007

Abstract

Background

Insulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified.

Results

We used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites.

Conclusion

Taken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture.