Genome-scale mapping and functional characterization of cis-regulatory networks in cellular reprogramming and regeneration

This project aims to enhance the regenerative capacity of certain recalcitrant DOE-target crops by leveraging genomics-enabled approaches to uncover and reprogram the gene regulatory networks (GRNs) governing somatic embryogenesis (SE), a process where plants regenerate from somatic cells. Our approach focuses on identifying the key genes and regulatory sequences in the genome that drive SE competency, such as transcription factors (TFs) and DNA control regions (cis-regulatory elements or CREs). To do this, we will construct and compare GRNs between plant varieties with high and low SE capacities, using advanced techniques that measure TF binding sites in the genome (DAP-seq), chromatin accessibility (single-cell ATAC-seq), and gene expression dynamics (single-cell RNA-seq). Specifically, we will (1) create a single-cell atlas of how gene expression and chromatin states change during SE; (2) Develop comprehensive CRE maps in the contrasting plant varieties for SE-relevant TFs and their complexes; (3) Infer and validate gene networks using in silico perturbation and CRISPR-based functional assays. The outcomes of this research could transform plant biotechnology by making it easier to engineer and breed valuable crops that currently resist genetic transformation. Our findings will provide new tools and knowledge to accelerate crop improvement, advancing genome engineering strategies, and expand our understanding of how plant genes function during regeneration.