Regulation of Arabidopsis chromatin organization by PDS5A

• Applicant: Professor Dr. Chang Liu
• Subject Area: Plant Genetics and Genomics
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 555595095

Eukaryote genomes in interphase nuclei are organized in a non-random, hierarchical fashion that correlates to gene expression and other biological activities in the nucleus. One key structural element in the three-dimensional (3D) chromatin organization is the Topologically Associating Domain (TAD), which facilitates the creation of distinct chromatin compartments and specific chromatin interactions, including those between enhancers and their target genes. While TAD-like structures are prevalent in many plant species, they have been curiously sparse in the model plant Arabidopsis thaliana. However, in our recent research, we discovered that the Arabidopsis pds5a mutant plant formed prominent TAD-like structures; additionally, we found that PDS5A is a key factor suppressing TAD-like structure formation. These findings served as a catalyst for the proposal of this project, which aims to unravel the underlying mechanisms of 3D chromatin organization in plants. Our project comprises three parts: Firstly, we will employ Micro-C technology to precisely identify the genomic and epigenomic factors associated with chromatin insulation and long-range chromatin loop formation in the TAD-enriched Arabidopsis mutant. Secondly, we will utilize various molecular techniques to explore the interactions between PDS5A and the genome, as well as to identify other proteins involved in this process. In the third part, we plan to dissect the formation of TAD-like structures in Arabidopsis across different cell cycle stages. In its entirety, we anticipate that our research will not only expand our understanding but also challenge the current paradigm in Arabidopsis genome organization, positioning our work at the forefront of functional genomics and offering insights into the intricacies of 3D plant chromatin organization.

• DFG Programme: Research Grants