The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE205112 | GEO | 2022/09/16
REPOSITORIES: GEO
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Project description:In eukaryotes, DNA is associated with histones to form nucleosomes, the basic component of the chromatin. This structure presents a physical barrier for nuclear proteins to access DNA and, therefore, its plays a critical role in multiple processes such as transcription, replication and repair. Eukaryotes have evolved multiple chromatin remodelers to control nucleosome position and composition like the SWI/SNF family, which has been studied in detailed in diverse model organisms. We recently uncovered an evolutionarily conserved SWI/SNF complex in plants reminiscent of the mammalian BAF subclass, which incorporates the ATPases MINU and signature subunits TPF. In this study we characterize the impact of TPF depletion in the model plant Arabidopsis and we explore the genomic targets of the BAF complex, as well as its impact on nucleosome position and gene expression. Our results show that TPF mutants have strong developmental phenotypes, suggesting an important role in the complex function. TPF and MINU genomic targets show change in the position of the +1 nucleosome towards the promoter when the complex is mutated. While there is little correlation between this shift and changes in gene expression levels, we find a strong correlation between +1 nucleosome shift and the presence of extended 5´ regions towards the promoter in hundreds of BAF targets, suggesting a change in TSS usage. These additional 5´ UTR regions might alter RNA function and be responsible for the strong developmental phenotypes observed in the TPF and MINU mutants.
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Project description:In eukaryotes, DNA is associated with histones to form nucleosomes, the basic component of the chromatin. This structure presents a physical barrier for nuclear proteins to access DNA and, therefore, its plays a critical role in multiple processes such as transcription, replication and repair. Eukaryotes have evolved multiple chromatin remodelers to control nucleosome position and composition like the SWI/SNF family, which has been studied in detailed in diverse model organisms. We recently uncovered an evolutionarily conserved SWI/SNF complex in plants reminiscent of the mammalian BAF subclass, which incorporates the ATPases MINU and signature subunits TPF. In this study we characterize the impact of TPF depletion in the model plant Arabidopsis and we explore the genomic targets of the BAF complex, as well as its impact on nucleosome position and gene expression. Our results show that TPF mutants have strong developmental phenotypes, suggesting an important role in the complex function. TPF and MINU genomic targets show change in the position of the +1 nucleosome towards the promoter when the complex is mutated. While there is little correlation between this shift and changes in gene expression levels, we find a strong correlation between +1 nucleosome shift and the presence of extended 5´ regions towards the promoter in hundreds of BAF targets, suggesting a change in TSS usage. These additional 5´ UTR regions might alter RNA function and be responsible for the strong developmental phenotypes observed in the TPF and MINU mutants.
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Project description:In eukaryotes, DNA is associated with histones to form nucleosomes, the basic component of the chromatin. This structure presents a physical barrier for nuclear proteins to access DNA and, therefore, its plays a critical role in multiple processes such as transcription, replication and repair. Eukaryotes have evolved multiple chromatin remodelers to control nucleosome position and composition like the SWI/SNF family, which has been studied in detailed in diverse model organisms. We recently uncovered an evolutionarily conserved SWI/SNF complex in plants reminiscent of the mammalian BAF subclass, which incorporates the ATPases MINU and signature subunits TPF. In this study we characterize the impact of TPF depletion in the model plant Arabidopsis and we explore the genomic targets of the BAF complex, as well as its impact on nucleosome position and gene expression. Our results show that TPF mutants have strong developmental phenotypes, suggesting an important role in the complex function. TPF and MINU genomic targets show change in the position of the +1 nucleosome towards the promoter when the complex is mutated. While there is little correlation between this shift and changes in gene expression levels, we find a strong correlation between +1 nucleosome shift and the presence of extended 5´ regions towards the promoter in hundreds of BAF targets, suggesting a change in TSS usage. These additional 5´ UTR regions might alter RNA function and be responsible for the strong developmental phenotypes observed in the TPF and MINU mutants.
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Project description:Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of the plant BAF-like complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of expressed genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5´-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcriptional start site (TSS) usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and upstream TSS usage suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and alternative TSS usage.
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Project description:The relationship between the positioning of nucleosomes and transcription start sites (TSSs) is unclear. Here, we report that deletion of the Fun30 class chromatin remodelers Fft2 and Fft3 leads to depletion of +1 nucleosome occupancy. Strikingly, in the vast majority of cases, this depletion had no impact on the placement of the TSS, favoring a model where TSS placement is primarily DNA sequence-driven.
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