BRD1, BRD2 and BRD13 are core subunits of Arabidopsis SWI/SNF complexes [ChIP-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA678631 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13065867_1.fastq.gz | Fastqsanger.gz | |||
| SRR13065867_2.fastq.gz | Fastqsanger.gz | |||
| SRR13065868_1.fastq.gz | Fastqsanger.gz | |||
| SRR13065868_2.fastq.gz | Fastqsanger.gz | |||
| SRR13065869_1.fastq.gz | Fastqsanger.gz |
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Project description:Switch defective/sucrose non-fermentable chromatin remodeling complexes are multi-subunit machines that play vital roles in regulating chromatin structure and gene expression. However, how SWI/SNF complexes recognize target loci is still not fully understood. Here, we show that Arabidopsis bromodomain-containing homologous proteins, BRD1, BRD2 and BRD13, are core subunits of SWI/SNF complexes that are required for SWI/SNF genomic targeting. The three BRDs directly interact with multiple SWI/SNF subunits, including the BRAHMA (BRM) catalytic subunit. Phenotypic and transcriptome analysis of the brd1 brd2 brd13 triple mutants showed that the BRDs act in large redundancy to control developmental processes and gene expression that are also regulated by BRM. BRDs extensively co-localize with BRM on chromatin. brd1 brd2 brd13 mutation results in the reduced BRM protein levels and genome-wide targeting on chromatin. Finally, we demonstrate that the bromodomain of BRD2 is essential for genomic targeting of BRD2, highlighting the role of this reader domain in the recruitment of BRM-containing SWI/SNF complexes to target sites in plants. SWI/SNF chromatin remodeling complexes are evolutionarily conserved and is confirmed to use the energy derived from hydrolysis of ATP to alter the density or the position of nucleosomes on the DNA or the composition of histone octamer. Bromodomain, an acetylated histone interaction module, was found in chromatin remodeling factors. During the 29 Arabidopsis bromodomain-containing protein, like GCN5 and GTE4/6, their function has been reported. Here, we reported three BRM-interacting bromodomain-containing protein, BRD1, BRD2 and BRD13 are new core subunits of Arabidopsis SWI/SNF complexes. brd1/2/13 displayed a similar phenotype like brm, such as down-ward curled leaves, reduced fertility, shorter silique and root. Moreover, brm brd1/2/13 shows more serious phenotype just like brm-1. Y2H, Co-IP, RNA-seq and ChIP-seq assay reveal that BRDs interact with BRM at both protein and chromatin level. Future more, BRDs are required for BRM genome-wide occupancy and BRM might bind to chromatin via BRDs bromodomain by interacting with their BBC domain.
2021-03-22 | GSE161515 | GEO
Project description:BRD1/2/13 are new core subunits of Arabidopsis SWI/SNF complexes
| PRJNA678860 | ENA
Project description:The SWI/SNF family of chromatin remodeling complexes is evolutionarily conserved and present in yeast, animals and plants. While the biological functions of plant SWI/SNF complexes have been studied in detail, their composition is still elusive. To clarify this picture we used protein extracts from Arabidopsis plants in vegetative phase of growth to perform a series of immunoprecipitation followed by mass spectrometry experiments, using GFP-tagged BRM ATPase as a bait. The analysis of MS data showed that the dominant form of SWI/SNF complex present in these extracts has a specific subunit composition including ARP4 and 7, SWI3C, SWP73B and BRIP2, as well as three bromodomain containing subunits, BRD1, 2 and 13. This subunit composition and the lack of the core SWI/SNF subunit BSH (SNF5/INI1) both strongly resemble the characteristics of the specific subclass of mammalian SWI/SNF complexes referred to as non-canonical BAFs, indicating that homologues of these complexes also exist in plants. We next found that depletion of the all three BRDs severely affected the assembly of this form of BRM-associated SWI/SNF complex. However, while BRD1 and BRD2 were found sufficient to allow complex formation, BRD13 was only required under BRD1/2 deficiency. The analyses of IP/MS results using BRM-GFP in different brd mutant backgrounds as well as BRD1-GFP indicate that SWI/SNF assemblies containing only one BRD isoform, BRD1 or BRD2, do exist. Furthermore, our data indicate that BRD1/2 may be necessary for the incorporation of BRIP2 subunit into the complex. Together, our results shed new light on the structural and functional diversification of SWI/SNF complexes in Arabidopsis.
2023-04-03 | PXD030928 | Pride
Project description:SWI/SNF chromatin remodelers are evolutionarily conserved multiprotein complexes that use the energy of ATP hydrolysis to change chromatin structure. A characteristic feature of SWI/SNF remodelers is the occurrence in both the catalytic ATPase subunit and some auxiliary subunits, of bromodomains, the protein motifs capable of binding acetylated histones. Here, we report that the Arabidopsis bromodomain-containing proteins BRD1, BRD2, and BRD13 are likely true SWI/SNF subunits that interact with the core SWI/SNF components SWI3C and SWP73B. Loss of function of each single BRD protein caused early flowering but had a negligible effect on other developmental pathways. By contrast, a brd triple mutation (brdx3) led to more pronounced developmental abnormalities, indicating functional redundancy among the BRD proteins. The brdx3 phenotypes, including hypersensitivity to abscisic acid and the gibberellin biosynthesis inhibitor paclobutrazol, resembled those of swi/snf mutants. Furthermore, the BRM protein level and occupancy at the direct target loci SCL3, ABI5, and SVP were reduced in the brdx3 mutant background. Finally, a brdx3 brm-3 quadruple mutant, in which SWI/SNF complexes were devoid of all constituent bromodomains, phenocopied a loss-of-function mutation in BRM. Taken together, our results demonstrate the relevance of BRDs as SWI/SNF subunits and suggest their cooperation with the bromodomain of BRM ATPase.
| S-EPMC8299063 | biostudies-literature
Project description:BRD1, BRD2, and BRD13 are likely subunits of Arabidopsis SWI/SNF chromatin remodeling complexes. To investigate the effect of disruption of BRD genes on global gene expression in Arabidopsis, we performed transcriptome profiling of 18-day-old single brd2, double brd1 brd2 and triple brdx3 mutants.
2021-03-01 | E-MTAB-9688 | biostudies-arrayexpress
Project description:Mitotic bookmarking by SWI/SNF subunits
| PRJNA783609 | ENA
Project description:For cells to initiate and sustain a differentiated state, it is necessary that a “memory” of this state is transmitted through mitosis to the daughter cells. Mammalian SWItch/ Sucrose Non- Fermentable (SWI/SNF) complexes, also called Brg1/ Brg- associated factors (BAF), control cell identity by modulating chromatin architecture to regulate gene expression, but whether they participate in cell fate memory is unclear. Here, we provide evidence that subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division. The SWI/SNF core subunits SMARCE1 and SMARCB1 are displaced from enhancers but bound on promoters during mitosis and we show that this binding is required for appropriate reactivation of bound genes after mitotic exit. Ablation of SMARCE1 during a single mitosis in mouse embryonic stem cells is sufficient to disrupt gene expression, impair the occupancy of several established bookmarks at a subset of their targets, and cause aberrant neural differentiation. Thus, SWI/SNF subunit SMARCE1 plays a mitotic bookmarking role and is essential for heritable epigenetic fidelity during transcriptional reprogramming.
2023-03-18 | GSE189563 | GEO
Project description:Loss of Swi/Snf subunits regulate transcription.
2017-02-17 | GSE81722 | GEO
Project description:The 12-subunit Swi/Snf chromatin remodeling complex is conserved from yeast to humans. It functions to alter nucleosome positions by either sliding nucleosomes on DNA or evicting histones. Interestingly, 20% of all human cancers carry mutations in subunits of the Swi/Snf complex. Many of these mutations cause protein instability and loss, resulting in partial Swi/Snf complexes. Although several studies have shown that histone acetylation and activator-dependent recruitment of Swi/Snf regulate its function, it is less well understood how subunits regulate stability and function of the complex. Using functional proteomic and genomic approaches, we have assembled the network architecture of yeast Swi/Snf. In addition, we find that subunits of the Swi/Snf complex regulate occupancy of the catalytic subunit Snf2, thereby modulating gene transcription. Our findings have direct bearing on how cancer-causing mutations in orthologous subunits of human Swi/Snf may lead to aberrant regulation of gene expression by this complex.
2017-08-07 | MSV000081418 | MassIVE
Project description:The 12-subunit Swi/Snf chromatin remodeling complex is conserved from yeast to humans. It functions to alter nucleosome positions by either sliding nucleosomes on DNA or evicting histones. Interestingly, 20% of all human cancers carry mutations in subunits of the Swi/Snf complex. Many of these mutations cause protein instability and loss, resulting in partial Swi/Snf complexes. Although several studies have shown that histone acetylation and activator-dependent recruitment of Swi/Snf regulate its function, it is less well understood how subunits regulate stability and function of the complex. Using functional proteomic and genomic approaches, we have assembled the network architecture of yeast Swi/Snf. In addition, we find that subunits of the Swi/Snf complex regulate occupancy of the catalytic subunit Snf2, thereby modulating gene transcription. Our findings have direct bearing on how cancer-causing mutations in orthologous subunits of human Swi/Snf may lead to aberrant regulation of gene expression by this complex.
2017-08-07 | MSV000081417 | MassIVE