Understanding organ identity in flowers at the level of single cells

• Applicant: Professorin Dr. Kerstin Kaufmann
• Subject Area: Plant Cell and Developmental Biology
• Term: from 2020 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 438774542

Cells in multicellular organisms typically contain the same genetic information, yet display an amazing variation in form and functions. In plants, most developmental processes occur post-embryonically, starting from pools of stem cells that are located in meristems. After floral transition, the Arabidopsis shoot apical meristem produces floral meristems that differentiate into four types of organ: sepals, petals, stamens and carpels. Past research has identified major transcription factors controlling organ specification and differentiation, yet their cell-type specific functions are still poorly understood. In this project, we will combine single cell and cell-type specific genomics techniques with targeted promoter analyses. The aim is to develop a molecular framework for cellular differentiation in flowers, including the characterization of major cell types, their developmental trajectories and the characterization of cell-type specific regulons. More specifically, we will measure mRNA expression at the level of single cells in wildtype and homeotic mutant flowers. To facilitate the classification of cell types, we will additionally employ mRNA-seq in specific GFP-labelled cell populations. The single cell RNA-seq data will allow the prediction of novel cell-type specific marker genes, which will be analyzed using dedicated reporter gene analyses in planta. In a complementary approach, we will analyze the activity of cis-regulatory regions using single cell ATAC-seq. We will generate scATAC-seq datasets for wildtype and homeotic mutant lines, and complement the data by ATAC-seq data from sorted cell populations. Thereby, we will obtain datasets that can be directly compared and integrated with the data from single cell RNA-seq, allowing the identification of combinations of regulatory elements that control cell-type specific gene expression patterns. These can then be validated in planta using reporter gene analysis in developing floral meristems and flowers. Together, the research plan proposed here will bring our understanding of organ specification in flowers to a new level, because we will be able to dissect cell- and organ-specific activities of homeotic transcription factors and predict the corresponding regulatory modules.

• DFG Programme: Research Grants