Final Report Summary - CELLPATTERN (The Cellular Basis of Multicellular Pattern Formation) Plants build their entire body from small groups of stem cells at the tips of shoot and root. While the activity of such plant stem cells has been described in some detail, it remains a mystery how these are initially formed. In the CELLPATTERN project, we used the early embryo of the flowering plant Arabidopsis thaliana to understand how the first stem cells and tissue precursors are formed and how the collective of genes activated in these cells define their unique cellular properties.Although the Arabidopsis thaliana embryo is an excellent model for studying the regulation of tissue and stem cell formation, and 3D tissue morphogenesis, it is very challenging to study this phase of development, because there are few cells, those cells are very small, and the embryo is deeply embedded in maternal seed and fruit tissues. Thus, a major component of this project involved the development of dedicated methodologies to measure gene activity at genome-wide level at the resolution of single cells, and to visualize entire cells and their content structures in 3D.In the first phase of the CELLPATTERN project, several new methodologies were successfully developed. In one part of the project, a genetic labeling method has allowed us to isolate precise populations of cell nuclei from unique cell types in the early embryo, and by using whole-genome expression profiling, we have been able to generate an “atlas” of gene activity for all genes in the Arabidopsis genome. Using this atlas, we have found how cell types differ from each other, and we have isolated genes that are active only in certain cell types, including the first stem cells. We have combined the information of which genes are activated in certain cell types with information on which genes are activated by important genetic regulators of early embryo development. This has lead to the identification of several new groups of proteins that control the cytoskeleton during oriented cell division.In a second part of the project, we have developed genetic tools and approaches to visualize volumes of all cells, as well as subcellular structures at high resolution in 3D. We have first used these to address the question of how cells determine their cell division plane. We found that many cells divide according to a default “rule” that follows from the 3D shape of the cell. We next discovered that the regulation of cell division orientation that is exerted by the plant hormone auxin, is based upon the ability of the hormone to prevent cells from division according to this default rule. This is a new concept in regulation of division orientation, and we have next used tools to visualize subcellular structures in default and non-default divisions. This has revealed a critical role for the reorganization of the cytoskeleton by the auxin hormone. Future studies will focus on how the hormone can manipulate the properties of the cytoskeleton to bring about oriented division.In summary, the CELLPATTERN project has generated new concepts in plant embryogenesis research, and the tools and approaches developed will be a major enabling factor for future studies in plant developmental biology.
