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

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 oligonucleotidebased 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.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). Prevailing models suggest that the SWI/SNF complexes are recruited to specific in vivo targets through interactions with DNA-binding transcription factors, where the ATP-dependent activities of the complex assist in gene regulation through changes in DNA-histone contacts (3, 4). Subsequently, the affected nucleosomes can be covalently modified to maintain active or repressed transcription through cooperation with histone acetyltransferases and histone deacetylase complexes (5).Whole genome analyses of yeast and mammalian SWI/SNF complex mutants revealed that the expression of ϳ5% of all genes was affected by removal of the complex (6, 7). Importantly, whereas there was a detectable reduction in the expression of a small subset of genes, more transcripts were induced upon loss of the gene encoding the core ATPase (SNF2/SWI2), suggesting that the complex had direct roles in both gene activation and repression. In fact, both epigenetic functions of the yeast complex appear to rely on the ATPase activity of SNF2/ SWI2 (8). Although the yeast SWI/SNF complex is not required for vegetative growth, the metazoan SWI/SNF complex counterparts, including the Brahma (Brm) complex in Drosophila (9, 10) and the related mammalian hBrm/Brg1 complexes (11), are essential (12, 13). This requirement may be due to direct involvement of the Brm complexes in facilitating global gene expression by RNA polymerase II (14).The snr1 gene (S...

The SWI/SNF complex and cancer

“…In Drosophila, SWI/SNF has been shown to regulate hormoneresponsive ecdysone-induced genes (Schwartz et al, 2004;Zraly et al, 2006). In mammalian cells, the glucocorticoid receptor has been functionally linked to the SWI/SNF complex (Muchardt and Yaniv, 1993;Ostlund Farrants et al, 1997;Trotter and Archer, 2004), and the re-expression of either BRG1 or BRM is sufficient to restore glucocorticoid receptor function in cells that lack both BRG1 and BRM (Glaros et al, 2007).…”

“…Although SWI/SNF is a relatively rare enzyme in yeast, present at only 100-500 copies per nucleus (Cote et al, 1994), it has been estimated that 5-7% of all yeast genes require SWI/SNF activity for expression (Sudarsanam et al, 2000;Zraly et al, 2006;Monahan et al, 2008). Estimates of the role of SWI/SNF in the control of Drosophila gene expression range from 1-2% of the genome (based upon inactivation of SNR1/ SNF5) to essentially the whole genome (based upon estimated chromosomal loss of RNA polymerase II in cells that express a dominant-negative brahma allele) (Armstrong et al, 2002).…”

Histone recognition and nuclear receptor co-activator functions ofDrosophilaCara Mitad, a homolog of the N-terminal portion of mammalian MLL2 and MLL3

“…4E). Chromatin immunoprecipitation using whole animal extracts prepared from early pupae expressing HA-CMI and antibodies to the HA epitope revealed that CMI was strongly enriched at the endogenous Hsp27 EcRE, but not at another ecdysone inducible gene (Eig71Eh-i promoter) (Wright et al, 1996;Zraly et al, 2006) that lacks an EcRE, or at a control (rp49) gene. We conclude that CMI is a hormone-dependent co-activator of nuclear receptorstimulated transcription.…”

“…and M.O.D., unpublished). To further our studies on epigenetic regulation of ecdysone target genes (Zraly et al, 2006), we searched for Drosophila genes that could encode a protein highly related to the N-terminal half of MLL2 and identified a single open reading frame (CG5591). We named the gene cara mitad (cmi; translated as 'dear half').…”

Beyond molting-roles of the steroid molting hormone ecdysone in regulation of memory and sleep in adult Drosophila

“…The developmental co-regulators of EcRs include TAIMAN (histone acetylase), 7 Trithorax-related (TRR) (histone lysine methyltransferase), 40 DART1 (histone arginine methyltransferases), 41 BRAHMA (ATP-dependent chromatin remodeler), 42 NURF (ATP-dependent chromatin remodeler), 43 and DEK (histone chaperone). 44 It will be interesting to examine whether these epigenetic factors, which influence EcR-mediated transcription in the nervous system during development, are likewise involved in transcriptional regulation in the nervous system in mature adult flies.…”