Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish [scRNA-seq]

Marbled crayfish (Procambarus virginalis) are a parthenogenetically reproducing, globally invasive freshwater crayfish species. Previous work has shown that the global population is characterized by a monoclonal genome, which raises important questions about the mechanisms that promote their invasiveness. Dnmt1 is an evolutionarily conserved DNA methyltransferase responsible for maintaining 5-methylcytosine (5mC) patterns across the genome. While its relevance in transcriptional regulation and cell fate specification is well established, its role in ecological adaptation remains poorly understood. Here we show that environmental changes lead to significant downregulation of Dnmt1 in marbled crayfish. When mimicking this effect through a dsRNA-based in vivo knockdown of Dnmt1, we observed that invasiveness-related behavioral traits, such as activity and boldness were enhanced. Using image cytometry and single-cell RNA sequencing, we also detected an increase in the most mature immune cell type, the granular cells and depletion of hemocyte-derived neuronal precursors, which support adult neurogenesis. Further analysis by whole-genome bisulfite sequencing showed that these phenotypic changes are underpinned by a global reduction in gene body DNA methylation and a dysregulation of genes involved in nervous and immune system functions. Additionally, we observed nucleosome destabilization as a key mechanism influencing transcriptional changes after methylation loss. Our findings highlight a role for Dnmt1 in the canalization of cellular and organismal phenotypes, and provide a paradigm for how downregulation of Dnmt1 can enhance invasive traits. Overall design: 28 days post injection of, 3 control animals (injected with dsGFP) and 3 Dnmt1 KD (injected with dsDNM1) were bled and the hemocytes isolated. 10 X genomics were used for single-cell RNA-sequencing.