{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T06:02:26Z","timestamp":1789970546188,"version":"4.0.1"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"\n Introduction<\/jats:title>\n \n We previously identified the silenced maize line\n p1-ww-id1<\/jats:italic>\n , which carries\n Ac killer 1<\/jats:italic>\n (\n Ack1<\/jats:italic>\n ), a naturally occurring inverted-repeat allele generated by alternative transposition.\n Ack1<\/jats:italic>\n produces\n Ac<\/jats:italic>\n -homologous small RNAs associated with reduced\n Ac<\/jats:italic>\n activity, but how these small RNAs relate to\n Ac<\/jats:italic>\n silencing across development remains unclear.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n We examined\n Ack1<\/jats:italic>\n -associated silencing across four developmental stages representing embryonic, juvenile vegetative, adult vegetative, and reproductive tissues.\n Ac<\/jats:italic>\n transcript abundance, region-specific small RNAs, and DNA methylation were analyzed, and\n Ack1<\/jats:italic>\n was introduced into a\n mop1<\/jats:italic>\n mutant background to test the contribution of the canonical 24-nt RNA-directed DNA methylation (RdDM) pathway.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Across all four developmental stages, the\n Ac<\/jats:italic>\n subterminal\/promoter region accumulated predominantly 24-nt small RNAs, whereas the Ac-transcribed region accumulated predominantly 21-22 nt small RNAs. Both regions gained CG, CHG, and CHH methylation despite their distinct small RNA compositions.\n Ac<\/jats:italic>\n transcript abundance was reduced across the developmental series, with significant repression in embryonic, juvenile, and adult vegetative tissues. In V8 leaf 10, loss of MOP1 depleted subterminal\/promoter 24-nt small RNAs and reduced DNA methylation in this region. In contrast, the\n Ac<\/jats:italic>\n -transcribed region accumulated more 21\u201322-nt small RNAs and showed increased DNA methylation, while\n Ac<\/jats:italic>\n remained transcriptionally repressed.\n <\/jats:p>\n <\/jats:sec>\n \n Discussion<\/jats:title>\n \n These findings reveal two epigenetically distinct regions of\n Ac<\/jats:italic>\n characterized by different predominant small RNA populations and contrasting responses to disruption of canonical RdDM. The results support a model in which a naturally occurring inverted-repeat allele organizes region-specific epigenetic states across an active transposon while transcriptional repression persists.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fpls.2026.1956494","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T05:36:40Z","timestamp":1789969000000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Ac killer 1 establishes two epigenetically distinct regions associated with stable silencing of the maize Ac transposon"],"prefix":"10.3389","volume":"17","author":[{"given":"Dafang","family":"Wang","sequence":"first","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sicong","family":"Wang","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilly","family":"Horowitz","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meixia","family":"Zhao","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuhair","family":"Ishraq","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte","family":"Huang","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Scelfo","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tejbir","family":"Singh","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan","family":"Singh","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sihun","family":"Kim","sequence":"additional","affiliation":[{"name":"Hofstra University","place":["Hempstead, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/nature04884","article-title":"An RNA-dependent RNA polymerase is required for paramutation in maize","volume":"442","author":"Alleman","year":"2006","journal-title":"Nature"},{"key":"B2","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1007\/s004380050410","article-title":"Maize Activator transposase has a bipartite DNA binding domain that recognizes subterminal sequences and the terminal inverted repeats","volume":"254","author":"Becker","year":"1997","journal-title":"Mol. 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