brahma: Biological Overview | Evolutionary Homologs | Regulation | Developmental Biology | Effects of Mutation | References

Gene name - brahma

Synonyms -

Cytological map position - 72A 3-4

Function - transcriptional activation

Keywords - trithorax group

Symbol - brm

FlyBase ID:FBgn0000212

Genetic map position - 3-43.0

Classification - DNA dependent ATPase - helicase motif

Cellular location - nuclear



NCBI links: Precomputed BLAST | Entrez Gene
Recent literature
Kwok, R.S., Li, Y.H., Lei, A.J., Edery, I. and Chiu, J.C. (2015). The catalytic and non-catalytic functions of the Brahma chromatin-remodeling protein collaborate to fine-tune circadian transcription in Drosophila. PLoS Genet 11: e1005307. PubMed ID: 26132408
Summary:
This study identifies the Brahma (Brm) complex as a regulator of the Drosophila clock. In Drosophila, CLOCK (CLK) is the master transcriptional activator driving cyclical gene expression by participating in an auto-inhibitory feedback loop that involves stimulating the expression of the main negative regulators, period (per) and timeless (tim). BRM functions catalytically to increase nucleosome density at the promoters of per and tim, creating an overall restrictive chromatin landscape to limit transcriptional output during the active phase of cycling gene expression. In addition, the non-catalytic function of BRM regulates the level and binding of CLK to target promoters and maintains transient RNAPII stalling at the per promoter, likely by recruiting repressive and pausing factors. By disentangling its catalytic versus non-catalytic functions at the promoters of CLK target genes, this study uncovers a multi-leveled mechanism in which BRM fine-tunes circadian transcription.

Kawaguchi, T. and Hirose, T. (2015). Chromatin remodeling complexes in the assembly of long noncoding RNA-dependent nuclear bodies. Nucleus [Epub ahead of print] PubMed ID: 26709446
Summary:
Paraspeckles are subnuclear structures that assemble on nuclear paraspeckle assembly transcript 1 (NEAT1) long noncoding (lnc)RNA. Paraspeckle formation requires appropriate NEAT1 biogenesis and subsequent assembly with multiple prion-like domain (PLD) containing RNA-binding proteins. SWI/SNF chromatin remodeling complexes (see Drosophila Brahma) were found to function as paraspeckle components that interact with paraspeckle proteins (PSPs) and NEAT1. SWI/SNF complexes play an essential role in paraspeckle formation that does not require their ATP-dependent chromatin remodeling activity. Instead, SWI/SNF complexes facilitate organization of the PSP interaction network required for intact paraspeckle assembly. SWI/SNF complexes may collectively bind multiple PSPs to recruit them onto NEAT1. SWI/SNF complexes are also required for Sat III (Satellite III) lncRNA-dependent formation of nuclear stress bodies under heat shock conditions. Organization of the lncRNA-dependent omega speckle in Drosophila also depends on the chromatin remodeling complex. These findings raise the possibility that a common mechanism controls the formation of lncRNA-dependent nuclear body architecture.

Ramachandran, S. and Henikoff, S. (2016). Transcriptional regulators compete with nucleosomes post-replication. Cell 165: 580-592. PubMed ID: 27062929
Summary:
Every nucleosome across the genome must be disrupted and reformed when the replication fork passes, but how chromatin organization is re-established following replication is unknown. To address this problem, Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq) was developed to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution. The characteristic chromatin landscape at Drosophila promoters and enhancers is lost upon replication. The most conspicuous changes are at promoters that have high levels of RNA polymerase II (RNAPII) stalling and DNA accessibility and show specific enrichment for the BRM remodeler. Enhancer chromatin is also disrupted during replication, suggesting a role for transcription factor (TF) competition in nucleosome re-establishment. Thus, the characteristic nucleosome landscape emerges from a uniformly packaged genome by the action of TFs, RNAPII, and remodelers minutes after replication fork passage.
Li, X., Yang, F., Chen, H., Deng, B., Li, X. and Xi, R. (2016). Control of germline stem cell differentiation by polycomb and trithorax group genes in the niche microenvironment. Development [Epub ahead of print]. PubMed ID: 27510973
Summary:
Polycomb and Trithorax group (PcG and TrxG) genes function to regulate gene transcription by maintaining the repressive or active chromatin state, respectively. This antagonistic activity is important for body patterning during embryonic development, but whether this function module has a role in adult tissues is unclear. This study reports that in the Drosophila oogenesis, disruption of the Polycomb responsive complex 1 (PRC1) specifically in the supporting escort cells causes blockage of cystoblast differentiation and germline stem cell- like tumor formation. The tumor is caused by derepression of decapentaplegic (dpp) which prevents cystoblast differentiation. Interestingly, activation of dpp in escort cells requires the function of TrxG gene brahma (brm), suggesting that loss of PRC1 in escort cells causes Brm-dependent dpp expression. This study suggests a requirement for balanced activity between PcG and TrxG in an adult stem cell niche, and disruption of this balance could lead to the loss of tissue homeostasis and tumorigenesis.
Hong, S.T. and Choi, K.W. (2016). Antagonistic roles of Drosophila Tctp and Brahma in chromatin remodelling and stabilizing repeated sequences. Nat Commun 7: 12988. PubMed ID: 27687497
Summary:
Genome stability is essential for all organisms. Translationally controlled tumour protein (TCTP) is a conserved protein associated with cancers. TCTP is involved in multiple intracellular functions, but its role in transcription and genome stability is poorly understood. This study demonstrates new functions of Drosophila TCTP (Tctp) in transcription and the stability of repeated sequences (rDNA and pericentromeric heterochromatin). Tctp binds Brahma (Brm) chromatin remodeler to negatively modulate its activity. Tctp mutants show abnormally high levels of transcription in a large set of genes and transposons. These defects are ameliorated by brm mutations. Furthermore, Tctp promotes the stability of repeated sequences by opposing the Brm function. Additional regulation of pericentromeric heterochromatin by Tctp is mediated by su(var)3-9 transcriptional regulation. Altogether, Tctp regulates transcription and the stability of repeated sequences by antagonizing excess Brm activity. This study provides insights into broader nuclear TCTP functions for the maintenance of genome stability.


BIOLOGICAL OVERVIEW

brahma, a member of the trithorax group (TRX-G) was initially isolated as a suppressor of Polycomb (Kennison, 1988). While Polycomb mutants fail to silence Antennapedia complex (ANTP-C) genes, trithorax mutants reverse this phenotype by failing to activate the same genes in a genetic game of "spy versus spy." brahma mutants cause developmental defects similar to other mutants which fail to express homeotic genes after embryogenesis, such as held out wings and loss of humeral bristles (Brizuela, 1994).

What is brahma's role in gene activation? To answer this question we first digress into the arcane world of the gene activation assay. There are two kinds. One uses naked DNA, not enshrouded with proteins, and the other uses chromatin, a complex of DNA and proteins in which proteins serves to restrict the access of transcription factors to their targets, the promoters of genes. Research carried out in yeast is enlightening since many of the 12 proteins found in the SWI/SNF complex of yeast have been purified and characterized. When SWI/SNF (pronounced switch-sniff) complex proteins are tested on naked DNA, the proteins act as a DNA dependent ATPase, that is they require naked DNA to harness the energy of ATP, which is required for some aspect of their function. The involvement of yeast SWI/SNF in overcoming the repressive affects of chromatin has recently been documented (Kruger, 1993). This study shows that mutating histones H3 and H4 (See Drosophila Histone H4 and Histone H3) partly relieve the requirement of the yeast SWI/SNF complex for transcription.

Brahma is homologous to yeast SWI2, a DNA-stimulated ATPase. Although both Brahma and yeast proteins have helicase domains, in no case has it been found that the helicase is functional. When they do work, helicases use the energy of ATP to unwind DNA. Despite the lack of a functional helicase domain the SWI/SNF yeast complex is still able to activate gene transcription. Although the ATPase activity is activated by naked DNA, SWI/SNF can activate gene transcription from DNA enshrouded with protein, that is SWI/SNF is able to overcome the repressive effect of chromatin to activate gene transcription (Tamkin 1995).

The second SWI2 homolog of Drosophila, ISWI, can be contrasted to Brahma, as it exists in a different gene activating complex. The ATPase activity of ISWI is activated by chromatin and not DNA; its concentration in the cell is 1000 times greater than that of Brahma, and ISWI's molecular weight is lower than that of Brahma because it lacks a C-terminal bromodomain, an important sequence domain that probably functions in protein-protein interaction. In addition, the protein complex that includes ISWI (NURF) is lower in molecular weight than the complex containing Brahma (Tsukiyama, 1995).

brahma, like yeast SWI/SNF, is part of a large protein complex. The newly identified SNR1 of Drosophila forms part of this complex. SNR1 is a homolog of yeast SNF5. Thus it is not an isolated protein that acts to activate gene transcription from chromatin but a large multi-protein complex. Both Brahma and SNR1 proteins are present in this complex as measured by their co-immunoprecipitation from Drosophila extracts (Dingwall, 1995).

It appears then, that there are two molecular machines for gene activation in Drosophila: 1) the SWI/SNF type complex, where ATPase activity depends on DNA and 2), the NURF complex, where ATPase activity relies on chromatin. Both of these protein complexes can activate transcription from chromatin, the protein enshrouded complex between DNA and protein. To date, these two complexes have yet to be fully explored. Very likely they each play a distinctive role in development, roles research efforts have yet to describe fully.

Loss of maternal brahma function blocks oogenesis; individuals homozygous for extreme brm alleles die as late embryos with no obvious pattern defects (Brizuella, 1994). Since it has not been possible to generate embryos lacking both maternal and zygotic brm function, the exact role of brm in embryonic development is not clear. Information concerning the role of brm after embryogenesis has been derived primarily from the analysis of hypomorphic brm alleles. Individuals trans-heterozygous for certain combinations of brm alleles survive to adulthood and exhibit developmental abnormalities similar to those arising from reduced expression of Antp-C and Bx-C genes, including the transformation of first legs to second legs and the fifth abdominal segment to a more anterior identity (Bruzuella, 1994). Because the effect of complete loss of brm function had not been examined, it was unclear whether brm is also involved in other processes. To clarify the role of brm in Drosophila development, mosaic analysis has been used to determine the null phenotype of brm mutations. As an alternative approach, site-directed mutagenesis was used to generate dominant-negative brm mutations and investigate the functions of evolutionarily conserved domains within the Brm protein (Elfring, 1998).

Using mosiac analysis, it has been found that the complete loss of brm function decreases cell viability and causes defects in the peripheral nervous system of the adult. The size and frequency of experimental clones in the head and thoracic segments are significantly reduced relative to the controls. In contrast, the frequency and size of control and experimental clones in the abdomen are similar. These data indicate that brm is essential for the development of imaginal tissues but not abdominal histoblasts. It is also possible that sufficient BRM RNA or protein persists after clone induction to allow the development of the abdominal segments. Examination of the phenotype of brm clones reveals unanticipated defects in the adult peripheral nervous system. The mechanosensory bristles of brm clones in the head, thoracic, and abdominal segments are either duplicated, stunted, or fused. In many cases, the sockets are also malformed, absent, or duplicated. No homeotic transformations have been observed in experimental clones in any of the abdominal segments. How might brm control the fate or proliferation of the cells that form mechanosensory organs? The simplest explanation is that brm regulates the activity of one or more neurogenic genes. Another possibility is that brm mutation disrupts regulation of the cell cycle. This is suggested by recent studies demonstrating that the human BRG1 and HBRM proteins cooperate with retinoblastoma tumor suppressor proteins to regulate cell cycle progression (see Retinoblastoma-family protein) (Elfring, 1998).

A dominant-negative brm mutation (DNbrm) was generated by replacing a conserved lysine in the ATP-binding site of the Brm protein with an arginine. This mutation eliminates brm function in vivo but does not affect assembly of the high molecular weight (2 million Daltons) Brm complex. Expression of the dominant-negative Brm protein causes peripheral nervous system defects, homeotic transformations, and decreased viability. Individuals bearing one or two copies of the dominant-negative Brm are viable, but frequently exhibit partial transformations of haltere to wing, as evidenced by an increase in haltere size and the appearance of ectopic bristles on the capitellum. Approximately one third of dominant-negative Brm adults exhibit this transformation, which is presumably caused by the decreased expression of the Ultrabithorax gene. Increasing the ratio of dominant-negative Brm to wild-type Brm to 2:1 is lethal. Thus, the dominant-negative brm mutation behaves as an antimorphic allele of brm. Expression of the dominant-negative Brm protein in patterns identical to the segmentation genes hairy or engrailed has no effect on embryonic viability or segmentation. The lack of an embryonic phenotype resulting from embryonic expression of the dominant-negative Brm protein may be caused by the high maternal expression of wild-type Brm protein, which is sufficient to allow embryogenesis to proceed to near completion in the absence of zygotic brm function. Expression of the dominant-negative protein in imaginal tissues after embryogenesis leads to greatly reduced viability. Individuals reared at 20° display partial transformation of first leg to second leg, as evidenced by a reduction in the number of sex comb teeth on the first leg. This phenotype is also seen in adults trans-heterozygous for hypomorphic brm alleles and is presumably caused by decreased expression of the Sex combs reduced (Scr) gene. Adults reared at 20° also display twinning of mechanosensory bristles, a phenotype similar to that observed in clones of brm2 tissue. Expression of the dominant negative protein also has dramatic effects on the size and morphology of the wing; mutant wings are reduced in size, and the L5 and the posterior cross-vein (PCV) are usually absent. Defects in the campaniform sensilla, a class of sensory organs important for flight, are also observed with high frequency. These defects fall into four classes: missing sensilla, duplication or triplication of sensilla, transformation of sensilla into bristles, and the appearance of ectopic sensilla. Ectopic sensilla and bristles are observed most frequently on the L3 vein. Three sensilla (L3-1, L3-2, and L3-3) and no bristles are normally found on this vein. By contrast, approximately one-half of mutant wings display one or two additional sensilla on L3. Ectopic bristles are observed on this vein in approximately one-fifth of mutant wings (Elfring, 1998).

Brahma regulates the Hippo pathway activity through forming complex with Yki-Sd and regulating the transcription of Crumbs

The Hippo signaling pathway restricts organ size by inactivating the Yorkie (Yki)/Yes-associated protein (YAP) family proteins. The oncogenic Yki/YAP transcriptional coactivator family promotes tissue growth by activating target gene transcription, but the regulation of Yki/YAP activation remains elusive. In mammalian cells, Brg1, a major subunit of chromatin-remodeling SWI/SNF family proteins, was identified that interacts with YAP. This finding led the authors to investigate the in vivo functional interaction of Yki and Brahma (Brm), the Drosophila homolog of Brg1. Brm was found to function at the downstream of Hippo pathway and interacts with Yki and Scalloped (Sd) to promotes Yki-dependent transcription and tissue growth. Furthermore, it was demonstrated that Brm is required for the Crumbs (Crb) dysregulation-induced Yki activation. Interestingly, it was also found that crb is a downstream target of Yki-Brm complex. Brm physically binds to the promoter of crb and regulates its transcription through Yki. Together, this study has shown that Brm functions as a critical regulator of Hippo signaling during tissue growth and plays an important role in the feedback loop between Crb and Yki (Zhu, 2014).

The core signaling cascade of Hippo pathway has been extensively studied. However, the regulatory mechanism of Yki/YAP activation remains largely elusive. This study found that Brm, a component of SWI/SNF complex, interacts with Yki and regulates organ growth in Drosophila. The findings indicated that Brm is indispensable for Yki activation to drive the expression of target genes. Interestingly, it was also found that the expression of crb is regulated by Yki-Brm complex. The ChIP assay showed that Brm and Yki physically bound to the promoter region of crb, and knockdown of Yki reduced the binding of Brm to crb promoter. Taken together, this study presents a novel feedback loop between Crb and the Yki-Brm complex. Thus, the mutual regulation between apical polarity and Hippo pathway could be critical for tissue growth and homeostasis (Zhu, 2014).

Considering the transcriptional co-dependence with RNA Polymerase II and broad localization in actively transcribed regions, the Brm complex may be present on multiple promoters and is required by global gene transcription. However, the expression of only 872 genes has been observed significantly altered by Brm knockdown. This suggests that there is a selectivity of Brm-mediated transcriptional regulation. In addition to Hippo pathway, morphogens, such as Wingless (Wg), Hedgehog (Hh) and Decapentaplegic (Dpp), also play fundamental roles in organ patterning and growth. Therefore, the readouts of Wg, Hh and Dpp pathway in wing discs with brm knockdown were examined. Interestingly, only Wg secretion was found to be altered, which argued that there was gene specificity of Brm-mediated transcription. Many other factors including the interaction of transcription factors and co-factors, histone modifications and DNA methylation have been also shown essential in this process. Therefore, how Brm regulates the specific targets transcription needs to be further investigated (Zhu, 2014).

These data demonstrate that the enhancement of Crb levels caused by yki overexpression can be suppressed by brm knockdown. However, the overexpression of Brm alone cannot alter the Crb levels. These results suggest that the regulatory function of Brm complex is indispensable for crb but relies on Yki. Together with the fact that Brm physically associate with Yki, it is argued that Brm complex is recruited to target gene promoters through Brm-Yki interaction. Accordingly, another Drosophila transcription factor Zeste has been reported that recruits the Brm complex to chromatin to initiate transcription. Beside of Brm, Moira (Mor), another subunit of the complex, has also been reported to directly interact with Yki and occupy on the promoters of Hpo target genes, which support the working model that Yki facilitates the recruitment of Brm complex onto crb promoters. Taken together, this study draws a conclusion that the specificity of Brm for regulating Hippo targets is determined by Yki recruitment. Given that both the Brm complex and Hippo pathway are conserved in mammals, these results shed a light on a conserved interaction, which might be critical for mammalian growth and tissue homeostasis (Zhu, 2014).


GENE STRUCTURE

cDNA clone length - 5266

Bases in 5' UTR - 55

Exons - five

Bases in 3' UTR - 297


PROTEIN STRUCTURE

Amino Acids - 1638

Structural Domains

Brahma has both a helicase domain that functions as a DNA-dependent ATPase and a bromodomain (Tamkun, 1995). The homology to Drosophila ISWI is high in the helicase domain, but ISWI, with a lower molecular weight than Brahma lacks the C-terminal bromodomain (Elfring, 1994).

The brm gene encodes a 1638 residue protein that is similar to SNF2/SWI2, a protein involved in transcriptional activation in yeast, suggesting possible models for the role of BRM in the transcriptional activation of homeotic genes. In addition, both BRM and SNF2 contain a 77 amino acid motif (the bromodomain) that is found in other Drosophila, yeast, and human regulatory proteins and may be characteristic of a new family of regulatory proteins (Tamkun, 1992).

In humans there are two SWI2 homologs, BRG1 and hbrm. BRG1 is present in a high-molecular-mass conplex of 2MD, similar in size to the yeast SWI/SNF complex. Two separate complexes contain either BRG1 or hbrm. The purified BRG1 of hbrm complexes contain 9-12 polypeptides. Like the yeast SWI/SNF complex, the complexes purified possess an ATP-dependent nucleosome disruption activity and are able to failitate transcription factor binding to mononucleosomes. Three proteins of the complex containing BRG1 have been purified, and termed BAFs (BRG1 associated factors). Two of the three, BAF170 and BAF155 are SWI3 homologs. They contain a tryptophan-repeat domain present in two or three tandem repeats in the myb family of proteins, but do not demonstrate DNA binding activity. A second conserved region is a predicted leucine-zipper region, possibly serving as a dimerization domain. BAF60 is a homolog of yeast SWP73, a novel SWI/SNF protein, and is homologous to a C.elegans protein. The subunit composition of BRG1 complex is different when purified from several different cell types (Wang, 1996a).


brahma: Evolutionary Homologs | Regulation | Developmental Biology | Effects of Mutation | References

date revised: 22 October 98 

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