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

Frank A Middleton,Claudia B Zraly,Andrew K Dingwall

doi:10.1074/jbc.m607806200

Frank A Middleton, Claudia B Zraly + Show 1 more

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https://doi.org/10.1074/jbc.m607806200

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Abstract

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.

Highlights

The metazoan SWI/SNF ATP-dependent chromatin remodeling complexes are large (1.2 MDa, 8 –11 subunits) multimeric assemblies that act to modify nucleosome structure, allowing for activation or repression of gene transcription [1, 2]
Removal of murine INI1 with an inverting allele leads to rapid (ϳ11 weeks) onset of rhabdoid tumors and T cell lymphomas with complete penetrance [38], whereas a conditional allele of snr1 leads to significantly increased growth [16]; SNR1/INI1 can be classified as a tumor/growth suppressor
We found that SNR1 functions to mediate aspects of Brm complex transcriptional repression in specific cells through shielding ATP-dependent gene activation, a mechanism that requires the coordinated activities of a tissue-specific transcription repressor and histone deacetylase activity [39]

Summary

Introduction

The metazoan SWI/SNF ATP-dependent chromatin remodeling complexes are large (1.2 MDa, 8 –11 subunits) multimeric assemblies that act to modify nucleosome structure, allowing for activation or repression of gene transcription [1, 2]. Cultured cell studies further suggested that the ecdysone-regulated genes, normally expressed late in development around the larval-pupal transition, were directly regulated by the Brm complex, which appears to function as a gene-specific corepressor in the absence of hormone.

Results

Conclusion