Cells are the building blocks of all living organisms and different cell types within an organism are defined by which of their genes they express. However, the precise gene expression profiles that define specific cell types are largely unknown. In addition, it is not known how cells come to express the set of genes that define one cell type versus another or whether the rules that specify cell types differ between plants and animals. This last question is especially interesting because being multicellular evolved independently in these two different kingdoms. The project will address these important questions by sequencing and analyzing mRNA from individual maize cells of different types, making these sequences and their methods and analytical procedures available to the wider plant research community. The project will also contribute to outreach and education by training undergraduate and high school students in genomics and computational biology as part of the Cold Spring Harbor Laboratory Undergraduate Research Program, which has a focus in quantitative biology, as well as the CSHL Partners For The Future Program, both of which train members of groups underrepresented in science. Students from each of these programs will be engaged in this project in both wet lab experiments and in bioinformatics and validation experiments, providing cross-disciplinary training in developmental biology and computational biology.
Living organisms develop and function by complex interactions between different specialized cell types. Using an optimized protocol to protoplast developing maize inflorescences, this team will isolate hundreds of thousands of single cells rapidly from different regions of this developing organ. The project will apply expertise in cell biology, genomics and single cell gene expression analysis to identify cell specific expression signatures in maize and to ask how cell type specification compares between plants and animals. A transformative new technology, single cell RNA sequencing (scRNA-seq), offers for the first time the opportunity to profile single plant cells and understand plant development at a fundamentally new level. This method has the power to understand cell type specific networks, to understand transcriptional heterogeneity within cell types and to identify novel regulators of cell fate. The project will test different scRNA-seq technologies and develop informatics tools that can be widely adopted by the plant community, and will be transformative in giving unique insights into single cell transcriptomes across different kingdoms of life. Therefore, this project has the potential to uncover the rules by which cell types are specified across kingdom wide scales. Data generated in this project will be openly available for reanalysis and integration with other datasets. The project will also develop and adapt single cell analysis methods that will be broadly applicable for the plant community.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
