Integrative Omics, Systems, and Synthetic Biology Approaches in Plant Science Session: Ronan O’Malley
Talk title: “The Gene Regulatory Landscape of Flowering Plants”
Talk abstract: The cistrome is a complete set of cis-regulatory elements (CREs) and transcription factors (TFs) within a genome. These components work in concert to manage gene expression in an organism. In our study, we've identified common cistrome features across a wide-range of flowering plants, which we refer to as the plant pancistrome. We achieved this through a novel technique we call multiplexed DNA affinity purification (multiDAP) sequencing. By pooling genomic DNA from ten diverse species, including Arabidopsis thaliana and relatives from the Brassicaceae family, as well as tomato, potato, poplar, strawberry, sorghum, and rice, we differentiated conserved TF-target gene relationships from species-specific ones, unveiling their evolutionary relatedness. In this plant pancistrome we observed that conserved TF-target gene relationships are heavily enriched for features associated with functional cis-regulatory elements. This evidence includes enrichment in open chromatin, target gene sets with expected Gene Ontology categories, and strong evidence that these regions are under evolutionary pressure to remain unchanged in A. thaliana. These findings contrast with the TF binding sites exclusive to A. thaliana, which lacked all such functional enrichment. By applying this pancistrome to annotate single-cell RNA-seq and ATAC-seq data collected across matching tissues from A. thaliana and three Brassicaceae relatives, we can produce cell-type resolved transcription factor regulatory networks shedding light for root, stem, leaf, and flower development, as well as hormonal response mechanisms. This comprehensive study underscores the pancistrome's utility as a robust tool for annotating cell type-specific TF regulatory pathways in flowering plants.
Bio: Dr. Ronan O’Malley completed both his BS and PhD in organic chemistry at the University of Chicago. He currently serves as an assistant professor in the Department of Human Genetics and is a member of the Genes, Genomes, and Systems Biology committee at the University of Chicago. Previously, he was a Group Lead at the Joint Genome Institute and principal investigator in the Environmental Genomics and Systems Biology division at Lawrence Berkeley National Laboratory. The O’Malley lab’s research centers on understanding the gene regulatory networks that underlie plant traits and investigating how these networks evolve to enable organisms to adapt to new environments and stresses. They employ functional genomic and epigenomic strategies—including single-cell genomics, high-throughput mutant screens, and DAP-seq, a technique Dr. O’Malley pioneered to detect transcription factor binding sites across the genome. Recently, the lab developed multiplexed DAP-seq (multiDAP), an innovation that enables tracing the evolutionary history of transcription factor binding sites. By applying multiDAP with single-nuclei RNA-seq and ATAC-seq across a range of species, the lab aims to build comprehensive atlases of plant, animal, and bacterial gene regulatory networks, ultimately working toward mechanistic models of stress response pathways to engineer climate-resilient plants.
Website: https://omalleylab.odoo.com