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J. Biol. Chem., Vol. 281, Issue 46, 35305-35315, November 17, 2006

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Hormone-response Genes Are Direct in Vivo Regulatory Targets of Brahma (SWI/SNF) Complex Function^*

Claudia B. Zraly, Frank A. Middleton, and Andrew K. Dingwall¹

From the Cardinal Bernardin Cancer Center, Oncology Institute and Department of Pathology, Loyola University of Chicago, Maywood, Illinois 60153 and the Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York 13210

Metazoan SWI/SNF chromatin remodeling complexes exhibit ATP-dependent activation and repression of target genes. The Drosophila Brahma (SWI/SNF) complex subunits BRM and SNR1 are highly conserved with direct counterparts in yeast (SWI2/SNF2 and SNF5) and mammals (BRG1/hBRM and INI1/hSNF5). BRM encodes the catalytic ATPase required for chromatin remodeling and SNR1 is a regulatory subunit. Importantly, SNR1 mediates ATP-independent repression functions of the complex in cooperation with histone deacetylases and direct contacts with gene-specific repressors. SNR1 and INI1, as components of their respective SWI/SNF complexes, are important for developmental growth control and patterning, with direct function as a tumor suppressor. To identify direct regulatory targets of the Brm complex, we performed oligonucleotide-based transcriptome microarray analyses using RNA isolated from mutant fly strains harboring dominant-negative alleles of snr1 and brm. Steady-state RNA isolated from early pupae was examined, as this developmental stage critically requires Brm complex function. We found the hormone-responsive Ecdysone-induced genes (Eig) were strongly misregulated and that the Brm complex is directly associated with the promoter regions of these genes in vivo. Our results reveal that the Brm complex assists in coordinating hormone-dependent transcription regulation of the Eig genes.

Received for publication, August 15, 2006 , and in revised form, September 7, 2006.

^* This work was supported National Science Foundation Grant MCB 0439316 and the Illinois Excellence in Academic Medicine Program (to A. K. D.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Tables S1-S11 and Figs. S1-S2.

¹ To whom correspondence should be addressed: Loyola University of Chicago Stritch School of Medicine, 2160 S. First Ave., Maywood, IL 60153. Tel.: 708-327-3141; Fax: 708-327-3342; E-mail: adingwall{at}lumc.edu.

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