Meeting Abstract
The 3D structure of chromatin is tightly linked to gene expression regulation. It is yet unclear how folding mechanisms may ensure robust and specific gene expression in non-vertebrate lineages. We aim to understand how the 3D folding of the genome impacts the cell-type specific transcriptional program via the interaction of cis-regulatory elements (CREs) with gene promoters. In order to do this, we have examined 3D chromatin structure, regulatory interactions and gene expression in an early-branching deuterostome Saccoglossus kowalevskii and the sea anemone Nematostella vectensis. We first identified CREs using ATAC-Seq and motif scanning computational methods and promoters via 5’ transcript mapping (Tn5Prime). We investigated regulatory interactions involving transcription factor (TF) promoters by performing Capture Hi-C. We computationally identified Saccoglossus TFs and characterized their binding specificity. We find that the use of alternative promoters is present in both Saccoglossus and Nematostella, possibly contributing to cell identity; TF promoters interact with multiple CREs in both species; and regulatory interactions spread through longer distances in Saccoglossus than in Nematostella. Our data has made progress in understanding the relationship between invertebrate 3D genome structure and regulatory interactions. Ultimately, we aim to combine our understanding of 3D gene regulation via CREs with developmental data on the role of TFs to generate a more complete picture of context-specific gene regulation in invertebrates.
