Spatiotemporal Regulation of Gene Expression during Plant Meristem Development

Plants are products of meristems. The root apical meristem (RAM) gives rise to the below-ground root system, while the shoot apical meristem (SAM) generates all the above-ground organs. The RAM and SAM contain highly organized stem cell niches, characterized by the presence of distinct cell types at various developmental stages. Meristems are thus ideal model tissues to study molecular regulatory mechanisms during development, via the generation of high-resolution expression atlases. In this dissertation, I aim to study the spatiotemporal regulation of gene expression during plant meristem development at a genome-wide level, including transcriptional regulation and post-transcriptional regulation. In my first study, high-throughput single cell RNA sequencing (scRNA-Seq) was used to build a cellular resolution gene expression atlas of the Arabidopsis root that includes all major cell types. In total, 4,727 single cell profiles were generated and analyzed. Developmental trajectories along root development were built. These depict a cascade of developmental progressions from stem cell to final differentiation. New regulators and downstream genes that define cell types or control cell state transition during the development were identified. This study demonstrates the power of applying scRNA- Seq to plants, and provides a unique spatiotemporal perspective of root cell differentiation. In my second study, a high-resolution maize shoot apex expression atlas in appendix II (Knauer et al., 2019) was used to investigate the spatiotemporal action of microRNAs (miRNAs) during development. Expression patterns of miRNA precursors and mature miRNA accumulation were examined, revealing that miRNA accumulation is regulated at both transcriptional and post-transcriptional level. Examples of the latter included effects on miRNA processing and/or stability in the vasculature and the stem cell population at the SAM tip, as well as the movement of miRNA within developing leaf primordia. By integrating data from RNA-Seq and degradome-Seq, a system was devised to predict the regulatory mechanism employed by miRNAs on their targets. This study provides a first comprehensive investigation of how the activity of the miRNAs that are critical to developmental pattern are regulated across space and time, revealing inputs from processes of regulating transcription, processing, stability, mobilities and miRNA efficacy.