mobilization threatens genome integrity. To survive, organisms have evolved silencing pathways capable of distinguishing self from non-self. This review emphasizes Caenorhabditis elegans
genome defense with a particular emphasis on systems-level detection of foreign DNA and the balance between silencing and protective pathways. Abundant small RNAs (piRNAs and siRNAs), aberrant DNA structures
(e.g., introns), and heterochromatin
domains largely mediate silencing. For example, CRISPR-based manipulation of endogenous piRNAs has elucidated precise targeting rules and a novel, conserved role in tuning endogenous germline
gene expression. Protective pathways are only just becoming clear: small RNA pathways (CSR-1), deamination
of endogenous dsRNA, and a pervasive, embedded DNA watermark (PATCs) can all counteract silencing to protect endogenous genes.