{"id":4012,"date":"2014-08-18T07:30:48","date_gmt":"2014-08-18T07:30:48","guid":{"rendered":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=4012"},"modified":"2014-08-18T07:30:48","modified_gmt":"2014-08-18T07:30:48","slug":"article-genome-biology","status":"publish","type":"post","link":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=4012","title":{"rendered":"Article: Genome Biology"},"content":{"rendered":"<p><a href=\"http:\/\/genomebiology.com\/2014\/15\/7\/411\/\">The black truffle methylome: non-exhaustive DNA methylation-mediated transposon silencing in a complex fungal genome with massive repeat element content<\/a>\u00a0B Montanini, PY Chen, M Morselli, A Jaroszewicz, D Lopez, F Martin, &#8230;\u00a0Genome Biology 15 (7), 411<\/p>\n<h1>Abstract<\/h1>\n<section>\n<div>\n<p style=\"text-align: justify;\">Background<\/p>\n<p style=\"text-align: justify;\">We investigated how an extremely transposon element (TE)-rich organism such as the plant-symbiotic ascomycete truffle\u00a0<em>Tuber melanosporum<\/em>\u00a0exploits DNA methylation to cope with the more than 45,000 repeated elements that populate its genome.<\/p>\n<h4 style=\"text-align: justify;\">Results<\/h4>\n<p style=\"text-align: justify;\">Whole-genome bisulfite sequencing performed on different developmental stages reveals a high fraction of methylated cytosines with a strong preference for CpG sites. The methylation pattern is highly similar among samples and selectively targets TEs rather than genes. A marked trend toward hypomethylation is observed for TEs located within a 1 kb distance from expressed genes, rather than segregated in TE-rich regions of the genome. Approximately 300 hypomethylated or unmethylated TEs are transcriptionally active, with higher expression levels in free-living mycelium compared to fruitbody. Indeed, multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs are found almost exclusively in free-living mycelium. A reduction of DNA methylation, restricted to non-CpG sites and accompanied by an increase in TE expression, is observed upon treatment of free-living mycelia with 5-azacytidine.<\/p>\n<h4 style=\"text-align: justify;\">Conclusions<\/h4>\n<p style=\"text-align: justify;\">Evidence derived from analysis of the\u00a0<em>T. melanosporum<\/em>\u00a0methylome indicates that a non-exhaustive, partly reversible, methylation process operates in truffles. This allows for the existence of hypomethylated, transcriptionally active TEs that are associated with copy number variant regions of the genome. Non-exhaustive TE methylation may reflect a role of active TEs in promoting genome plasticity and the ability to adapt to sudden environmental changes.<\/p>\n<p>&nbsp;<\/p>\n<\/div>\n<\/section>\n<section><a name=\"sec1\"><\/a><\/section>\n","protected":false},"excerpt":{"rendered":"<p>The black truffle methylome: non-exhaustive DNA methylation-mediated transposon silencing in a complex fungal genome with massive repeat element content\u00a0B Montanini, PY Chen, M Morselli, A Jaroszewicz, D Lopez, F Martin, &#8230;\u00a0Genome Biology 15 (7), 411 Abstract Background We investigated how &hellip; <a href=\"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=4012\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[],"class_list":["post-4012","post","type-post","status-publish","format-standard","hentry","category-academic-productions"],"_links":{"self":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/4012","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=4012"}],"version-history":[{"count":0,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/4012\/revisions"}],"wp:attachment":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4012"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4012"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4012"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}