brahma

EVOLUTIONARY HOMOLOGS

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Vertebrate Brahma homologs

Two highly related human cDNAs, hSNF2 alpha and -beta, encode amino acid sequences homologous to both yeast SWI2/SNF2 and Drosophila brahma. Similar to their yeast and Drosophila counterparts, both human cDNAs contain helicase motifs, a bromodomain, a highly charged C-terminal sequence and an N-terminal sequence rich in proline, glutamine and glycine (Chiba, 1994).

brahma has two human homologs: BRG1 and HBRM. BRG1 encodes a 205K nuclear protein and contains extensive homology to SWI2 and Drosophila BRG1 is exclusively nuclear and present in a high M(r) complex of about 2 x 10(6). The SWI2 family DNA-dependent ATPase domain evinces a functional conservation between yeast and humans. This suggests that a SWI/SNF protein complex is required for the activation of selective mammalian genes (Khavari, 1993).

The second human/Drosophila homolog, a counterpart of SNF2/SWI2, exists in mice as well. The human protein, designated hbrm, is a 180 kDa nuclear factor that can function as a transcriptional activator when fused to a heterologous DNA binding domain. The mouse homolog of hbrm was expressed in all mouse organs tested while hbrm was detected in some but not all investigated human cell lines. In cells failing to express the endogenous gene, transfected hbrm cooperates with the glucocorticoid receptor (GR) in transcriptional activation. However, hbrm had no effect on the activity of several other transcription factors, including the homeoprotein HNF-1. The co-operation between HBRM and GR required the DNA binding domain of GR and two separated regions of the HBRM protein, including a domain with homology to known helicases (Muchardt, 1993).

A human homolog of Saccharomyces cerevisiae SNF5 can be co-immunoprecipitated with hbrm, a homolog of Drosophila Brahma. The interaction between the two proteins is dependent on the region conserved between the human and the yeast SNF5s. Human SNF5 is a nuclear protein. The long glutamine- and proline-rich N-terminal region of the yeast protein is missing in the human protein. The interaction between hSNF5 and hbrm is dependent on the N-terminal region of hbrm. This region is by itself able to activate transcription when tethered to DNA and is important for cooperation between hbrm and the glucocorticoid receptor. This region is composed of two overlapping domains. The first domain is rich in prolines and glutamines. It is present in all SNF2/SWI2-related proteins, but the exact positioning of the amino acids varies from protein to protein. The second domain is composed of a succession of negatively and positively charged stretches. Inside this region, sequences for hbrm and another human Brahma homolog , BRG-1, are close to identity (Muchardt, 1995).

Distinct complexes of nine to 12 proteins (referred to as BRG1-associated factors [BAFs]) have been purified from several mammalian cell lines using an antibody to the SWI2-SNF2 homolog BRG1. Microsequencing reveals that the 47 kDa BAF is identical to INI1. Previously, INI1 has been shown to interact with and activate human immunodeficiency virus integrase and to be homologous to the yeast SNF5 gene. A group of BAF47-associated proteins were affinity purified with antibodies against INI1/BAF47 and were found to be identical to those co-purified with BRG1, strongly indicating that this group of proteins associates tightly and is likely to be the mammalian equivalent of the yeast SWI-SNF complex. Complexes containing BRG1 can disrupt nucleosomes and facilitate the binding of GAL4-VP16 to a nucleosomal template similar to the yeast SWI-SNF complex. Purification of the complex from several cell lines demonstrates that it is heterogeneous with respect to subunit composition. The two SWI-SNF2 homologs, BRG1 and hbrm, are found in separate complexes. Certain cell lines completely lack BRG1 and hbrm, indicating that they are not essential for cell viability and that the mammalian SWI-SNF complex may be tailored to the needs of a differentiated cell type (Wang, 1996b).

There are two mammalian homologs of the yeast SNF2-SWI2 subunit protein: SNF2alpha-brm and SNF2beta-BRG1; overexpression of either one has been shown to enhance transcriptional activation by glucocorticoid, estrogen, and retinoic acid (RA) receptors in transiently transfected cells. The function of SNF2beta-BRG1 has been investigated in the RA receptor-retinoid X receptor-mediated transduction of the retinoid signal in F9 embryonal carcinoma (EC) cells, which differentiate into endodermal-like cells upon RA treatment. The two SNF2beta-BRG1 alleles were targeted by homologous recombination and subsequently disrupted by using a conditional Cre recombinase. The F9 EC cells inactivated on both SNF2beta alleles were not viable and heterozygous mutant cells were affected in proliferation but not in RA-induced differentiation. Thus, in F9 EC cells, SNF2beta-BRG1 appears to play an essential role in basal processes involved in cell proliferation, in addition to its putative role in the activation of transcription mediated by nuclear receptors (Sumi-Ichinose, 1997).

The brm and BRG-1 proteins are mutually exclusive subunits of the mammalian SWI-SNF complex. Within this complex, they provide the ATPase activity necessary for transcriptional regulation by nucleosome disruption. Both proteins have recently been found to interact with the p105Rb tumor suppressor gene product, suggesting a role for the mammalian SWI-SNF complex in the control of cell growth. The expression of brm, but not BRG-1, is negatively regulated by mitogenic stimulation, and growth arrest of mouse fibroblasts leads to increased accumulation of the brm protein. The expression of this protein is also down-regulated upon transformation by the ras oncogene. Re-introduction of brm into ras transformed cells leads to partial reversion of the transformed phenotype by a mechanism that depends on the ATPase domain of the protein. These data suggest that increased levels of brm protein favour cell withdrawal from the cell cycle, whereas decreased expression of the brm gene may facilitate cellular transformation by various oncogenes. The persistence of BRG-1, but not brm, is essential for the viability of early embryonic cells. The persistence of BRG-1 in faster growing cells, and the accumulation of brm in cells that become slow growing or arrested, raises the possibility that a partial switch from BRG-1 to brm-containing SWI-SNF complexes occurs when cells slow their growth. brm may facilitate the expression of genes that are important for the maintenance of the quiescent or terminally differentiated state (Muchardt, 1998).

Mutation of Brahma homologs

The yeast and animal SNF-SWI and related multiprotein complexes are thought to play an important role in processes (such as transcription factor binding to regulatory elements) that require nucleosome remodeling in order to relieve the repressing effect of packaging DNA in chromatin. There are two mammalian homologs of the yeast SNF2-SWI2 subunit protein: SNF2alpha-brm and SNF2beta-BRG1. Overexpression of either protein has been shown to enhance transcriptional activation by glucocorticoid, estrogen, and retinoic acid (RA) receptors in transiently transfected cells. The function of SNF2beta-BRG1 has been investigated in the RA receptor-retinoid X receptor-mediated transduction of the retinoid signal in F9 embryonal carcinoma (EC) cells ,which differentiate into endodermal-like cells upon RA treatment. The two SNF2beta-BRG1 alleles were targeted by homologous recombination and subsequently disrupted by using a conditional Cre recombinase. F9 EC cells inactivated on both SNF2beta alleles are not viable and heterozygous mutant cells are affected in proliferation but not in RA-induced differentiation. Thus, in F9 EC cells, SNF2beta-BRG1 appears to play an essential role in basal processes involved in cell proliferation, in addition to its putative role in the activation of transcription mediated by nuclear receptors (Sumi-Ichinose, 1997).

The mouse Etl1 gene encodes a nuclear protein belonging to the rapidly growing SNF2/SWI2 family. Members of this family are related to helicases and nucleic-acid-dependent ATPases and have functions in essential cellular processes such as transcriptional regulation, maintenance of chromosome stability and various aspects of DNA repair. The ETL1 protein is expressed from the two-cell stage onward, throughout embryogenesis in a dynamic pattern with particularly high levels in the thymus, epithelia and the nervous system and in most adult tissues. As a first step to address the role of ETL1 in cells and during development, the gene was inactivated by homologous recombination. ES cells and mice lacking detectable ETL1 protein are viable, indicating that ETL1 is not essential for cell survival or for embryonic development. However, mutant mice show retarded growth, peri/post natal lethality, reduced fertility and various defects in the sternum and vertebral column. Expressivity and penetrance of all observed phenotypes are influenced by the genetic background. Isogenic 129SvPas mice lacking ETL1 have a severely reduced thoracic volume, which might lead to respiratory failure and could account for the high incidence of perinatal death on this genetic background (Schoor, 1999).

Animal SWI2/SNF2 protein complexes containing either the brahma (BRM) or brahma-related gene 1 (BRG1) ATPase are involved in nucleosome remodelling and may control the accessibility of sequence-specific transcription factors to DNA. In vitro studies have indicated that BRM and BRG1 regulate the expression of distinct sets of genes. However, since mice lacking BRM are viable and fertile, BRG1 might efficiently compensate for BRM loss. By contrast, because Brg1-null fibroblasts are viable but Brg1-null embryos die during the peri-implantation stage, BRG1 might exert cell-specific functions. To further investigate the in vivo role of BRG1, Brg1 was selectively ablated in keratinocytes of the forming mouse epidermis. BRG1 is selectively required for epithelial-mesenchymal interactions in limb patterning, and during keratinocyte terminal differentiation, in which BRM can partially substitute for BRG1. By contrast, neither BRM nor BRG1 are essential for the proliferation and early differentiation of keratinocytes, which may require other ATP-dependent nucleosome-remodelling complexes. Finally, it has been demonstrated that cell-specific targeted somatic mutations can be created at various times during the development of mouse embryos cell-specifically expressing the tamoxifen-activatable Cre-ER^T2 recombinase (Indra, 2005).

ATP-dependent chromatin-remodeling complexes contribute to the proper temporal and spatial patterns of gene expression in mammalian embryos and therefore play important roles in a number of developmental processes. SWI/SNF-like chromatin-remodeling complexes use one of two different ATPases as their catalytic subunit: brahma (BRM, also known as SMARCA2) and brahma-related gene 1 (BRG1, also known as SMARCA4). A floxed Brg1 allele was conditionally deleted with a Tie2-Cre transgene, which is expressed in developing hematopoietic and endothelial cells. Brg1^fl/fl:Tie2-Cre⁺ embryos die at midgestation from anemia, as mutant primitive erythrocytes fail to transcribe embryonic α- and β-globins, and subsequently undergo apoptosis. Additionally, vascular remodeling of the extraembryonic yolk sac is abnormal in Brg1^fl/fl:Tie2-Cre⁺ embryos. Importantly, Brm deficiency does not exacerbate the erythropoietic or vascular abnormalities found in Brg1^fl/fl:Tie2-Cre⁺ embryos, implying that Brg1-containing SWI/SNF-like complexes, rather than Brm-containing complexes, play a crucial role in primitive erythropoiesis and in early vascular development (Griffin, 2008).

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