Fly brm knockdown
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Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted MNase digestion followed by next-generation sequencing (NGS) to analyse the nucleosome profile in both control and Brm knockdown fly larvae.
2014-05-08 | E-MTAB-1967 | biostudies-arrayexpress
Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted next-generation sequencing (NGS) to analyse the expression profile in both control and Brm knockdown fly larvae.
2014-05-08 | E-MTAB-1966 | biostudies-arrayexpress
Project description:Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with the Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be restored mainly by SPT6LΔtSH2, which binds to TSS in a RNA polymerase II (Pol II)-independent manner. Furthermore, SPT6L and SYD/BRM are involved in regulating the nucleosome and Pol II occupancy around TSS. The presence of SPT6L is sufficient to restore the association of the chromatin remodeler SYD to chromatin and maintain normal nucleosome occupancy. Our findings suggest that the two chromatin remodelers can form protein complexes with the core subunit of the transcription machinery and regulate nucleosome occupancy in the early transcription stage.
2022-12-01 | GSE207391 | GEO
Project description:SWI/SNF chromatin remodeling complexes control gene expression by regulating chromatin structure. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we show that BRAHMA Interacting Protein 1 (BRIP1) and BRIP2 in Arabidopsis thaliana are core subunits of plant SWI/SNF complexes. BRIP1 and 2 are two homolog proteins. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome strikingly similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and 2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and 2 physically interact with BRM-containing SWI/SNF complexes, and extensively co-localize with BRM at endogenous genes. Loss-of-brip1brip2 results in decreased BRM occupancy at almost all BRM target genes and substantially reduced subunits incorporation into the BRM-containing SWI/SNF complexes. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants, and uncovers the essential role of these subunits in regulating the integrity (assembly) of SWI/SNF complexes in plants.
2020-06-21 | GSE142621 | GEO
Project description:Synthesis and accumulation of seed storage proteins (SSPs) is an important aspect of the seed maturation program. Genes encoding SSPs are specifically and highly expressed in the seed during maturation. However, the mechanisms that repress the expression of these genes in leaf tissue are not well understood. To gain insight into the repression mechanisms, we have performed a transgenic screening for mutants that express SSPs in leaves. Here we show that mutations of BRAHMA (BRM), a SNF2 chromatin remodelling ATPase, cause the ectopic expression of a subset of SSPs and other embryogenesis related genes in leaf tissue. Consistent with the notion that such SNF2-like ATPases form protein complexes in vivo, we observed similar phenotypes for mutations of AtSWI3C, a BRM interacting partner, and BSH, a SNF5 homolog and essential SWI/SNF subunit. Further, we present chromatin immunoprecipitation evidence that BRM is recruited to the promoters of a number of embryogenesis genes including the 2S genes, which are expressed/elevated in brm leaves. Consistent with its role in nucleosome remodelling, BRM appears to control the chromatin structure of the At2S2 promoter. These results show that a BRM-containing chromatin remodelling ATPase complex is involved in the direct repression of SSPs in leaf tissue. A matrix comprising the signal intensity value of each gene per replicate hybridization and the averaged data of each gene generated from three replicate hybridizations of the wild type and mutant samples, respectively, is linked below as a supplementary file. Experiment Overall Design: Total RNA was isolated from three independent biological replicates of essp3 mutant and Wild type (Pro?CG:GUS)) respectively. Three ATH1 chips were used for the mutant and three for the wild type.
2009-02-07 | E-GEOD-11505 | biostudies-arrayexpress
Project description:ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers, and the role of ATP hydrolysis in this process remain unclear. We used live-cell imaging of Drosophila polytene nuclei to monitor Brahma (BRM) remodeler interactions with its chromosomal targets. In parallel, we measured local chromatin condensation and its effect on BRM association. Surprisingly, only a small portion of BRM is bound to chromatin at any given time. BRM binds decondensed chromatin but is excluded from condensed chromatin, limiting its genomic search space. BRM-chromatin interactions are highly dynamic, whereas histone-exchange is limited and much slower. Intriguingly, loss of ATP hydrolysis enhanced chromatin retention and clustering of BRM, which was associated with reduced histone turnover. Thus, ATP hydrolysis couples nucleosome remodeling to remodeler release, driving a continuous transient probing of the genome.
2022-01-20 | PXD025474 | Pride
Project description:Interventions: Case series:Nucleosome Complex CAR-T cells
Primary outcome(s): Tumor markers
Study Design: Sequential
| 2684952 | ecrin-mdr-crc
Project description:Chromatin remodeling complexes control the availability of DNA binding sites to transcriptional regulators. Two distinct forms of the major SWI/SNF-related complex that have different activities in vitro can be distinguished by the presence of specific accessory subunits. In Drosophila, the core Brahma complex associates either with Osa to form the BAP complex, or with Bap170 and Bap180 to form the PBAP complex. Mutations affecting the core subunits have stronger developmental phenotypes than osa mutations; these differences could be due to PBAP complex activity . We have generated mutations in the genes encoding the PBAP-specific subunits Bap170 and Bap180 in order to study their functions in vivo. Bap180 is not essential for viability, but is required in ovarian follicle cells for normal eggshell development. Bap170 is necessary to stabilize the Bap180 protein; however, a mutant form that retains this function is sufficient for survival and fertility. The two subunits act redundantly to allow metamorphosis; using gene expression profiling of double mutants, we have found that the PBAP complex regulates genes involved in tissue remodeling and immune system function. Finally, we have generated mutants that lack Bap170, Bap180 and Osa in the germline to demonstrate that the function of the core Brahma complex in oogenesis does not require any of these accessory subunits. To study PBAP specific subunits Bap170 and Bap180 role in Drosophila melanogaster development Experiment Overall Design: Two males and two females for each genotype (wild type and bap170;bap180 double mutant) were processed at white prepupae stage (0 hour APF)
2009-10-21 | E-GEOD-11825 | biostudies-arrayexpress