Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family

The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. We discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD domain. We functionally demonstrate how retrotransposon encoded MBDs preferentially bind to CpG-dense methylated regions, which correspond to transposable element regions of the host genome, in the myriapod Strigamia maritima. Consistently, MBD-encoding Copia retrotransposons (CopiaMBD) are inserted in regions with higher CpG-densities than other LTR elements. This suggests that retrotransposons use MBDs to integrate into heterochromatic regions in Strigamia, avoiding potentially harmful insertions into host genes. In contrast, CopiaMBD insertions in the spider Stegodyphus dumicola genome accumulate in methylated gene bodies, given that transposons are not actively targeted by DNA methylation in the spider genome. Together, these data demonstrate that retrotransposons can co-opt host-derived epigenome readers, harnessing the host epigenome landscape to advantageously tune the retrotransposition process.