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DNA methylation also plays a major role in the regulation of gene expression. This dual role can come into conflict, where DNA methylation in gene regulatory regions becomes perturbed due to transposable element transposition, leading to disruption of gene expression. Here, we describe how this conflict is reflected in DNA methylation patterns in the sand lizard genome where there is recent transposable element activity. Using long-read sequencing technology we show that CpG islands in gene transcriptional start sites are typically hypomethylated and associated with higher gene expression. Outside transcriptional start sites, a majority of CpG islands overlapped transposable elements and were associated with hypermethylation, consistent with a host defence role in suppressing transposition activity. We identify 605 instances where transcriptional start sites were associated with transposable elements (4.3% of all genes). These instances were far rarer in conjunction with a CpG island, when methylation signatures would be in conflict. Transposable elements were found to be closer to and at higher density, the more hypermethylated a transcriptional start site was, suggesting strong selection against selfish genetic elements transposing into hypomethylated transcriptional start sites.<\/jats:p>","DOI":"10.1093\/jeb\/voag085","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T13:00:10Z","timestamp":1788440410000},"source":"Crossref","is-referenced-by-count":0,"title":["Interplay between the role of DNA methylation in regulating gene expression and TE silencing in a reptilian methylome"],"prefix":"10.1093","author":[{"given":"Joshua","family":"Hufton","sequence":"first","affiliation":[{"name":"Animal Ecology, Department of Ecology and Genetics, Uppsala University , Uppsala ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1911-8351","authenticated-orcid":false,"given":"Arild","family":"Husby","sequence":"additional","affiliation":[{"name":"Evolutionary Biology, Department of Ecology and Genetics, Uppsala University , Uppsala ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malavi","family":"Sengupta","sequence":"additional","affiliation":[{"name":"Animal Ecology, Department of Ecology and Genetics, Uppsala University , Uppsala ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mats","family":"Olsson","sequence":"additional","affiliation":[{"name":"Department of Biological and Environmental Sciences, University of Gothenburg , Gothenburg ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8714-0812","authenticated-orcid":false,"given":"Mette","family":"Lillie","sequence":"additional","affiliation":[{"name":"Animal Ecology, Department of Ecology and Genetics, Uppsala University , Uppsala ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"issue":"7","key":"2026101908564382900_bib1","doi-asserted-by":"publisher","first-page":"1127","DOI":"10.1093\/bioinformatics\/btu775","article-title":"Genomation: A toolkit to summarize, annotate and visualize genomic intervals","volume":"31","author":"Akalin","year":"2015","journal-title":"Bioinformatics"},{"key":"2026101908564382900_bib2","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/j.tig.2022.02.009","article-title":"Taming transposable elements in vertebrates: From epigenetic silencing to 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