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Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish


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.

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Data availability

Single-cell RNA sequencing (scRNA-seq) data generated in this study have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession code GSE295870 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE295870]. Whole-genome bisulfite sequencing (WGBS) data generated in this study are available in GEO under accession code GSE295869 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE295869]. Bulk RNA sequencing (RNA-seq) data generated in this study have been deposited in GEO under accession code GSE295871 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE295871]. MNase-seq data generated in this study are available in GEO under accession code GSE295867 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE295867]. The image cytometry data generated in this study have been deposited in the Zenodo database under (https://doi.org/10.5281/zenodo.18771566). Source data are provided in this paper.

Code availability

Data analyses were performed using publicly available software packages and published analysis pipelines as described in the Methods section. No custom software was developed for this study.

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Acknowledgements

We gratefully acknowledge Laura Wiegand, Areeba Khan and Nicole Schneider for technical support with the knockdown and behavioral experiments, as well as Steffen Schmitt and Tobias Rubner from the DKFZ Flow Cytometry Core Facility for support and guidance with the Image Cytometer. We also thank the Genomics and Proteomics Core Facility and the Single-Cell Open Lab for assistance with the sequencing experiments, as well as Jan-Phillip Mallm, Karsten Rippe and Vladimir Teif for the help with the MNase-Seq protocol and analysis using NucTools.

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Open Access funding enabled and organized by Projekt DEAL.

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J.J.D.L and V.C collected samples, performed experiments and analyzed the data. K.H. and G.R. provided technical and bioinformatical assistance, respectively. V.C. and F.L conceived the study. J.J.D.L and F.L wrote the paper with input from other authors. All authors approved the final manuscript.

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Frank Lyko.

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Diaz-Larrosa, J.J., Carneiro, V., Hanna, K. et al. Dnmt1 mediates epigenetic restriction of invasive traits in clonal crayfish.
Nat Commun (2026). https://doi.org/10.1038/s41467-026-71049-z

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