Integrative analysis of Hydra head regeneration reveals actions of conserved signaling pathways and transposable elements

Abstract

The extent to which animals can regenerate cells, tissues, or body parts varies largely. Hydra has a remarkable ability to undergo full body regeneration. Bisected polyps can regenerate the head and foot, and whole polyps can form from aggregates of cells. This capability is made possible by a cluster of cells known as the head organizer. Previous studies have found Wnt3 and other developmental genes associated with head organizer function. Yet, the genetic and molecular mechanisms of regenerating Hydra heads remain unresolved. In this study, we used bulk RNA-seq, bulk ATAC-seq, and single-cell RNA-seq from a regeneration time course to characterize the gene expression, gene regulation, molecular, and cellular features of Hydra head regeneration. WGCNA modules and cis-regulation of candidate head organizer genes identified genes co-expressed with Wnt3 and transcription factors important for regeneration. At the single-cell level, we identified at least six distinct cell types in the regenerating head tissue and characterized the expression of candidate genes. With these combined data sets, we identify and clarify some of the interactions between JNK, Wnt3, and EGRF signaling during Hydra head regeneration. Our study reveals coordination of early wound response, developmental transcription factors, and transposable elements during Hydra tissue regeneration and provides insight into the evolution of regeneration programs.