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In particular, hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress evolutionary novel, X-linked, meiotic drive loci. The consequences of deleting even a single hpRNA (<jats:italic>Nmy<\/jats:italic>) in males are profound, as such individuals are nearly incapable of siring male progeny. Here, comparative genomic analyses of <jats:italic>D<\/jats:italic>. <jats:italic>simulans<\/jats:italic> and <jats:italic>D<\/jats:italic>. <jats:italic>melanogaster<\/jats:italic> mutants of the core RNAi factor <jats:italic>dcr-2<\/jats:italic> reveal a substantially expanded network of recently-emerged hpRNA-target interactions in the former species. The <jats:italic>de novo<\/jats:italic> hpRNA regulatory network in <jats:italic>D<\/jats:italic>. <jats:italic>simulans<\/jats:italic> provides insight into molecular strategies that underlie hpRNA emergence and their potential roles in sex chromosome conflict. In particular, our data support the existence of ongoing rapid evolution of Nmy\/Dox-related networks, and recurrent targeting of testis HMG-box loci by hpRNAs. Importantly, the impact of the endo-RNAi network on gene expression flips the convention for regulatory networks, since we observe strong derepression of targets of the youngest hpRNAs, but only mild effects on the targets of the oldest hpRNAs. These data suggest that endo-RNAi are especially critical during incipient stages of intrinsic sex chromosome conflicts, and that continual cycles of distortion and resolution may contribute to speciation.<\/jats:p>","DOI":"10.1371\/journal.pgen.1010787","type":"journal-article","created":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T22:06:27Z","timestamp":1687385187000},"page":"e1010787","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":13,"title":["Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts"],"prefix":"10.1371","volume":"19","author":[{"given":"Jeffrey","family":"Vedanayagam","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ching-Jung","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ranjith","family":"Papareddy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Nodine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex S.","family":"Flynt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1249-6456","authenticated-orcid":true,"given":"Jiayu","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8432-5851","authenticated-orcid":true,"given":"Eric C.","family":"Lai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,6,21]]},"reference":[{"issue":"4997","key":"pgen.1010787.ref001","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1126\/science.1998119","article-title":"The evolution of sex chromosomes","volume":"251","author":"B. 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