The Drosophila Brahma (SWI/SNF) chromatin remodeling complex exhibits cell-type specific activation and repression functions

The Brahma (Brm) complex of Drosophila melanogaster is a SWI/SNF-related chromatin remodeling complex required to correctly maintain proper states of gene expression through ATP-dependent effects on chromatin structure. The SWI/SNF complexes are comprised of 8-11 stable components, even though the SWI2/SNF2 (BRM, BRG1, hBRM) ATPase subunit alone is partially sufficient to carry out chromatin remodeling in vitro. The remaining subunits are required for stable complex assembly and/or proper promoter targeting in vivo. Our data reveals that SNR1 (SNF5-Related-1), a highly conserved subunit of the Brm complex, is required to restrict complex activity during the development of wing vein and intervein cells, illustrating a functional requirement for SNR1 in modifying whole complex activation functions. Specifically, we found that snr1 and brm exhibited opposite mutant phenotypes in the wing and differential misregulation of genes required for vein and intervein cell development, including rhomboid, decapentaplegic, thick veins, and blistered, suggesting possible regulatory targets for the Brm complex in vivo. Our genetic results suggest a novel mechanism for SWI/SNF-mediated gene repression that relies on the function of a 'core' subunit to block or shield BRM (SWI2/SNF2) activity in specific cells. The SNR1-mediated repression is dependent on cooperation with histone deacetylases (HDAC) and physical associations with NET, a localized vein repressor.     

The Drosophila SNR1 (SNF5/INI1) subunit directs essential developmental functions of the Brahma chromatin remodeling complex

The Drosophila melanogaster Brahma (Brm) complex, a counterpart of the Saccharomyces cerevisiae SWI/SNF ATP-dependent chromatin remodeling complex, is important for proper development by maintaining specific gene expression patterns. The SNR1 subunit is strongly conserved with yeast SNF5 and mammalian INI1 and is required for full activity of the Brm complex. We identified a temperature-sensitive allele of snr1 caused by a single amino acid substitution in the conserved repeat 2 region, implicated in a variety of protein-protein interactions. Genetic analyses of snr1(E1) reveal that it functions as an antimorph and that snr1 has critical roles in tissue patterning and growth control. Temperature shifts show that snr1 is continuously required, with essential functions in embryogenesis, pupal stages, and adults. Allele-specific genetic interactions between snr1(E1) and mutations in genes encoding other members of the Brm complex suggest that snr1(E1) mutant phenotypes result from reduced Brm complex function. Consistent with this view, SNR1(E1) is stably associated with other components of the Brm complex at the restrictive temperature. SNR1 can establish direct contacts through the conserved repeat 2 region with the SET domain of the homeotic regulator Trithorax (TRX), and SNR1(E1) is partially defective for functional TRX association. As truncating mutations of INI1 are strongly correlated with aggressive cancers, our results support the view that SNR1, and specifically the repeat 2 region, has a critical role in mediating cell growth control functions of the metazoan SWI/SNF complexes.     

SNR1 is an essential subunit in a subset of Drosophila brm complexes,targeting specific functions during development

The snr1 gene of Drosophila melanogaster encodes a conserved component of the multiprotein Brahma (Brm) complex, a counterpart to the SWI/SNF complexes that participate in ATP-dependent chromatin remodeling. Loss-of-function and null mutations in the snr1 gene reveal its essential role in Drosophila development. We identified new mutant alleles and ectopically expressed deleted forms to dissect the specific functions of SNR1. Somatic and germ cell clone analyses confirmed its requirement in a continuous and widespread fashion for proper cell fate determination and oogenesis. Expression of SNR1 transgenes revealed unexpected roles in wing patterning, abdomen development, oogenesis, and sustained adult viability. A widespread distribution of SNR1 and BRM on the salivary gland polytene chromosomes showed that the Brm complex associated with many genes, but not always at transcribed loci, consistent with genetic data suggesting roles in both gene activation and repression. Despite essential Brm complex functions in leg development, genetic and protein localization studies revealed that snr1 was not required or expressed in all tissues dependent on Brm complex activities. Thus, SNR1 is essential for some, but not all Brm functions, and it likely serves as an optional subunit, directing Brm complex activity to specific gene loci or cellular processes.     

Cardiac genes show contextual SWI/SNF interactions with distinguishable gene activities

Recent experimental evidence indicates that cardiac and chromatin remodeling are associated with changes in gene expression mediated by Brahma-related gene 1 (Brg1), a member of the large group of SWI/SNF subunits. The second catalytic member of this family is Brahma (Brm), which shares close sequence homology to Brg1. Despite the sequence similarities, these determinants are found in distinct regulatory complexes; however, the precise nature and role of these remodeling enzymes in the failing heart remains unknown. Here we have hypothesized that Brg1 and Brm form distinct complexes in regulating gene expression in an animal model of cardiac hypertrophy. We have identified that the hypertrophic myocardium is characterized by profound morphological changes associated with increased expression of ANP (Nppa), BNP (Nppb) and β-MHC (Myh7) genes, correlating with reduced expression of the α-MHC (Myh6) and SERCA2A (Atp2a2) genes. Histone deacetylase inhibition prevented left ventricular hypertrophy indicating that the re-expression of gene activity can be associated with both contextual and distinct SWI/SNF interactions. We hypothesize that cardiac hypertrophy and the fetal gene expression program are associated with distinguishable binding of Brm and Brg1 on genes present in distinct complexes, suggesting possible independent-regulatory roles.     

Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits

Protein complexes of the SWI/SNF family remodel nucleosome structure in an ATP-dependent manner. Each complex contains between 8 and 15 subunits, several of which are highly conserved between yeast, Drosophila, and humans. We have reconstituted an ATP-dependent chromatin remodeling complex using a subset of conserved subunits. Unexpectedly, both BRG1 and hBRM, the ATPase subunits of human SWI/SNF complexes, are capable of remodeling mono-nucleosomes and nucleosomal arrays as purified proteins. The addition of INI1, BAF155, and BAF170 to BRG1 increases remodeling activity to a level comparable to that of the whole hSWI/SNF complex. These data define the functional core of the hSWI/SNF complex.