Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single cell level

Abstract

Gene regulatory networks (GRNs) can be used to describe gene interactions of various complex biological processes such as embryonic development, regeneration and disease. The purple sea urchinStrongylocentrotus purpuratusendomesoderm developmental GRN has been a 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 lacked information on whether 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, including whether the interactions are direct. 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 forSp-Pdx1positive cells in the 2 dpf gastrula embryonic gut and show that the previously studied GRN of the sea urchin embryonic hindgut is deeper and more complex than previously indicated.

Recent molecular techniques to strengthen ecological studies in echinoderms

“…These multi-omics approaches enable the exploration of gene functions, metabolic pathways, and ecological interactions within the microbial communities associated with echinoderms (Rey-Campos et al, 2022). By combining different molecular techniques, researchers can unravel the intricate relationships between echinoderms and their microbial partners, shedding light on the mechanisms driving their symbiotic associations and ecological contributions (Lowe et al, 2017;Voronov et al, 2023). On the other hand, the use of 16S rRNA sequencing has significantly advanced our understanding of the microbiota residing in the digestive systems.…”