Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish

TL;DR

This study shows that reduced DNA methylation in marbled crayfish increases their invasive traits by altering cell behavior and gene regulation.

Contribution

The study identifies Dnmt1 as a key epigenetic regulator of invasiveness in a clonal species.

Findings

Dnmt1 downregulation leads to increased invasive behaviors in marbled crayfish.

Loss of DNA methylation causes changes in immune and nervous system gene expression.

Reduced methylation is linked to nucleosome destabilization and altered cell differentiation.

Abstract

Procambarus virginalis (marbled crayfish) is a parthenogenetically reproducing invasive crayfish species. Its global population is monoclonal, which raises questions about the mechanisms promoting their invasiveness. Here we show that environmental changes downregulate the highly conserved Dnmt1 DNA methyltransferase in marbled crayfish. When phenocopying this effect through a dsRNA-based in vivo knockdown, we observe enhanced invasiveness-related behavioral traits. Image cytometry and single-cell RNA sequencing reveal an expansion of mature granular immune cells and depletion of hemocyte-derived neuronal precursors, which support adult neurogenesis. Whole-genome bisulfite sequencing shows that these phenotypes coincide with a global loss of gene body DNA methylation and dysregulation of nervous and immune system genes. Additionally, we observe nucleosome destabilization to be associated with transcriptional changes after methylation loss. Taken together, our findings identify Dnmt1 as a potential canalizer of cellular and organismal phenotypes, thus providing a framework for how epigenetic mechanisms modulate invasiveness.

The role of epigenetics in rapid adaptation remains poorly understood. This study shows that reduced Dnmt1-mediated DNA methylation in the clonal marbled crayfish alters chromatin organization, cell differentiation, and increases invasive behaviours.

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