The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site selection in Arabidopsis [ChIP-seq]

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. Overall design: Immunoprecipitated chromatin from inflorescences of Col-0, TPF2-3xFLAG and 3xFLAG-MINU2 lines were used to build libraries using the Nugen Ultralow V2 kit and sequenced at SE50. For histone ChIPs one replicate was done. For TPF2 and MINU2 ChIPs two independent transgenic lines were used as replicates compared to untransformed Col-0 plants.