An integrative multi-omics approach to draft gene regulatory networks at a cell type resolution

Gene regulatory networks (GRNs) can be used to describe gene interactions of various complex biological processes such as embryonic development, regeneration and disease. The GRN orchestrating endomesoderm development in the purple sea urchin Strongylocentrotus purpuratus pre-gastrula embryo has been the subject of multiple studies. Traditional approaches to drafting GRNs require embryological knowledge pertaining to the cell type families, information on the regulatory genes that control the regulatory state of the cell type family, causal data from gene knockdown experiments and validations of the identified interactions by cis-regulatory analysis, which helps identify the cis-regulatory modules (CRMs) of the regulatory genes. These approaches, while powerful, lack information on whether the majority of these gene interactions are direct. The advent of a multitude of omics approaches involving next-generation sequencing (-seq) allows to obtain the necessary information for GRN drafting. Here we present a combinatorial omics method for in silico GRN drafting at high resolution, using i) a single cell RNA-seq derived cell atlas highlighting the 2 day post fertilization (dpf) sea urchin gastrula cell type families, as well as the genes expressed at single cell level, ii) a set of putative CRMs and transcription factor (TF) binding sites obtained from chromatin accessibility ATAC-seq data, and iii) interactions directionality obtained from differential bulk RNA-seq following knockdown of the TF Sp-Pdx1, a key regulator of gut patterning in sea urchins. Using this method, we draft the GRN for the hindgut Sp-Pdx1 positive cells in the 2 dpf gastrula embryo. Overall, our combinatorial approach highlights the complex connectivity of the posterior gut GRN as postulated in the past and increases the resolution of gene regulatory cascades operating within it. ### Competing Interest Statement The authors have declared no competing interest.