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Molecular and Cellular Biology, July 2009, p. 3556-3568, Vol. 29, No. 13
0270-7306/09/$08.00+0     doi:10.1128/MCB.01748-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription{triangledown} ,{dagger}

Nan Jiang,1 Eldon Emberly,2 Olivier Cuvier,3 and Craig M. Hart1*

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803,1 Physics Department, Simon Fraser University, Burnaby, British Columbia, Canada,2 CNRS, Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, UPS, 31062 Toulouse cedex 04, France3

Received 14 November 2008/ Returned for modification 14 December 2008/ Accepted 9 April 2009

Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the presence of RNA polymerase II, dimethylated histone H3 K4, and the alternative histone H3.3. Forty percent of these genes are also associated with the polymerase negative elongation factor NELF. Like NELF-associated genes, most BEAF-associated genes are highly expressed. Using quantitative reverse transcription-PCR, we found that the expression levels of most BEAF-associated genes decrease in embryos and cultured cells lacking BEAF. These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels.

* Corresponding author. Mailing address: Department of Biological Sciences, 202 Life Sciences Building. Louisiana State University. Baton Rouge, LA 70803. Phone: (225) 578-7389. Fax: (225) 578-2597. E-mail: chart4{at}lsu.edu

{triangledown} Published ahead of print on 20 April 2009.

{dagger} Supplemental material for this article may be found at http://mcb.asm.org/.

Molecular and Cellular Biology, July 2009, p. 3556-3568, Vol. 29, No. 13
0270-7306/09/$08.00+0     doi:10.1128/MCB.01748-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Core, L. J., Lis, J. T. (2009). Paused Pol II captures enhancer activity and acts as a potent insulator. Genes Dev. 23: 1606-1612 [Abstract] [Full Text]  
  • Gurudatta, B. V., Corces, V. G. (2009). Chromatin insulators: lessons from the fly. Brief Funct Genomic Proteomic 8: 276-282 [Abstract] [Full Text]  


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