Towards an Understanding of Transcription Factors Controlling Arabidopsis Embryogenesis
Falko Hofmann1, Subramanian Paulraj1 and Michael Nodine1,*
1Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
Similar to animals the basic plant body plan is established during embryogenesis. Pattern formation is mainly orchestrated by the spatial and temporal regulation of gene expression. However, genetic screens in Arabidopsis thaliana (Arabidopsis) performed over the last decades have identified only a few dozen transcription factors (TFs) required for proper morphogenesis. This is presumably due to functional redundancy within large TF gene families. Furthermore, early embryonic tissue is difficult to recover, which limits the molecular biological experiments that can be performed on this tissue. We therefore adapted low input next generation sequencing techniques, such as Smart-seq2 and ATAC-seq, that can be applied across different developmental timepoints to obtain an integrated view of TF activity during embryogenesis.
Upon analyzing the transcriptome of Arabidopsis embryos, we identified hundreds of TFs that are differentially regulated across embryogenesis. Integrating our transcriptome data with ATAC-seq from embryos and known TF-binding occupancy, we identified more than 100 TFs with binding sites putatively enriched in embryo-specific open chromatin. This set contains previously reported and potentially novel master regulators of embryogenesis. By using a combination of large-scale datasets we are modeling their activity and performing mechanistic studies on selected candidates.
Funding: ERA-CAPS Grant Agreement no. 291864; Austrian Science Fund (FWF grant number 1476-B16)