{"id":1032,"date":"2026-04-19T15:17:32","date_gmt":"2026-04-19T15:17:32","guid":{"rendered":"https:\/\/www.embl.org\/groups\/genomics\/?page_id=1032"},"modified":"2026-06-16T07:40:29","modified_gmt":"2026-06-16T07:40:29","slug":"genome-wide-chromatin-and-dna-methylation-analysis","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/genomics\/genome-wide-chromatin-and-dna-methylation-analysis\/","title":{"rendered":"Genome-wide chromatin and DNA methylation analysis"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-1\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p>Genome-wide chromatin and DNA methylation analysis refers to a set of sequencing-based methods that map how the genome is regulated, not just what the DNA sequence is. Chromatin assays measure features such as DNA accessibility and protein\u2013DNA interactions that influence which genomic regions are active, while DNA methylation assays measure chemical modifications on DNA that help control gene activity and maintain cellular identity. Together, these approaches provide a genome-wide view of regulatory states and epigenetic changes across cell types, developmental stages, or experimental conditions.<\/p>\n\n\n<style>\n    <\/style>\n\n<section id=\"wp-block-1\">\n  <div class=\"vf-card-container vf-card-container__col-4 | vf-u-fullbleed  \n  | vf-u-background-color-ui--white \">\n        <div class=\"vf-card-container__inner\">\n            <div class=\"vf-section-header | vf-u-margin__bottom--600 | vf-u-sr-only\">\n        <h2 class=\"vf-section-header__heading\" >\n        Cards    <\/h2>\n              <\/div>\n      \n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Genome-wide chromatin analysis    <\/h3>\n                <p class=\"vf-card__text\">Assays that profile chromatin organization and regulatory activity across the genome, such as open chromatin regions, transcription factor binding, and histone modifications, helping identify active promoters, enhancers, and other regulatory elements.<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Genome-wide DNA methylation analysis    <\/h3>\n                <p class=\"vf-card__text\">Assays that measure cytosine methylation patterns across the genome to reveal epigenetic regulation, cell-type specific methylation signatures, and methylation changes associated with development, environment, or disease.<\/p>\n      <\/div>\n<\/article>\n\n\n\n          <\/div>\n      <\/div>\n<\/section>\n\n\n<h3 class=\"wp-block-heading\"><\/h3>\n\n\n<style>\n    <\/style>\n\n<section id=\"wp-block-2\">\n  <div class=\"vf-card-container vf-card-container__col-4 | vf-u-fullbleed  \n  | vf-u-background-color-ui--white \">\n        <div class=\"vf-card-container__inner\">\n            <div class=\"vf-section-header | vf-u-margin__bottom--600 | vf-u-sr-only\">\n        <h2 class=\"vf-section-header__heading\" >\n        Key References    <\/h2>\n              <\/div>\n      \n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Key References    <\/h3>\n                <p class=\"vf-card__text\"><ul>\r\n \t<li><strong>\u00a0<\/strong>&#8220;<a class=\"vf-card_link\" href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC3899983\/\"><em>Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays<\/em><\/a>&#8220;<\/li>\r\n \t<li>&#8220;<em><a class=\"vf-card_link\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/21744305\/\">Roles of lineage-determining transcription factors in establishing open chromatin: lessons from high-throughput studies<\/a><\/em>&#8220;<\/li>\r\n<\/ul><\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Key References    <\/h3>\n                <p class=\"vf-card__text\"><ul>\r\n \t<li>&#8220;<a class=\"vf-card_link\" href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC4926291\/\"><em>Profiling genome-wide DNA methylation<\/em><\/a>&#8220;<\/li>\r\n \t<li>&#8220;<a class=\"vf-card_link\" href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC6481677\/\"><em>DNA methylation signatures as biomarkers of prior environmental exposures<\/em><\/a>&#8220;<\/li>\r\n<\/ul><\/p>\n      <\/div>\n<\/article>\n\n\n\n          <\/div>\n      <\/div>\n<\/section>\n\n\n<div class=\"vf-grid | vf-grid__col-2\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<a href=\"https:\/\/www.embl.org\/groups\/genomics\/#Applications\" target=\"_blank\">\n<button class=\"vf-button vf-button--primary\">More applications<\/button>\n<\/a>\n<!--\/vf-button-->\n\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":19,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-1032","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages\/1032","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/users\/19"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/comments?post=1032"}],"version-history":[{"count":8,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages\/1032\/revisions"}],"predecessor-version":[{"id":1676,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/pages\/1032\/revisions\/1676"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/media?parent=1032"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/genomics\/wp-json\/wp\/v2\/embl_taxonomy?post=1032"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}