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Transposable elements are known to play important roles in genome evolution, yet questions remain as to how transposable elements alter genome structure and affect gene expression. Previous studies have shown that genome rearrangements can be induced by Reversed Ends Transposition involving termini of Activator and related transposable elements in maize and other plants. Here, we show that complex alleles can be formed by the rapid and progressive accumulation of Activator-induced duplications and rearrangements. The p1 gene enhancer in maize can induce ectopic expression of the nearby p2 gene in pericarp tissue when placed near it via different structural rearrangements. By screening for p2 expression, we identified and studied 5 cases in which multiple sequential transposition events occurred and increased the p1 enhancer copy number. We see active p2 expression due to multiple copies of the p1 enhancer present near p2 in all 5 cases. The p1 enhancer effects are confirmed by the observation that loss of p2 expression is correlated with transposition-induced excision of the p1 enhancers. We also performed a targeted Chromosome Conformation Capture experiment to test the physical interaction between the p1 enhancer and p2 promoter region. Together, our results show that transposon-induced rearrangements can accumulate rapidly and progressively increase genetic variation important for genomic evolution.<\/jats:p>","DOI":"10.1093\/genetics\/iyac124","type":"journal-article","created":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T11:36:20Z","timestamp":1663328180000},"source":"Crossref","is-referenced-by-count":16,"title":["Complex chromosomal rearrangements induced by transposons in maize"],"prefix":"10.1093","volume":"223","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6785-7071","authenticated-orcid":false,"given":"Sharu Paul","family":"Sharma","sequence":"first","affiliation":[{"name":"Department of Genetics, Development and Cell Biology, Iowa State University , Ames, IA 50011 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9933-7556","authenticated-orcid":false,"given":"Thomas","family":"Peterson","sequence":"additional","affiliation":[{"name":"Department of Genetics, Development and Cell Biology, Iowa State University , Ames, IA 50011 , USA"},{"name":"Department of Agronomy, Iowa State University , Ames, IA 50011 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,16]]},"reference":[{"issue":"1","key":"2024091617270765200_iyac124-B1","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1093\/genetics\/131.1.199","article-title":"Insertional mutagenesis of the maize P gene by intragenic transposition of Ac","volume":"131","author":"Athma","year":"1992","journal-title":"Genetics"},{"issue":"9","key":"2024091617270765200_iyac124-B2","first-page":"637","article-title":"Kernel pattern in variegated pericarp maize and the frequency of self-colored offspring","volume":"39","author":"Anderson","year":"1952","journal-title":"Am J 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