{"id":26170,"date":"2012-09-05T18:30:14","date_gmt":"2012-09-05T16:30:14","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=26170"},"modified":"2024-04-10T14:23:40","modified_gmt":"2024-04-10T12:23:40","slug":"fast-forward-for-biomedical-research","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/fast-forward-for-biomedical-research\/","title":{"rendered":"Fast forward for biomedical research"},"content":{"rendered":"\n<p>Today, an international team of researchers reveal that much of what has been called \u2018junk DNA\u2019 in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. Without these switches, genes would not work \u2013 and mutations in these regions might lead to human disease. Discovered by hundreds of scientists working on the&nbsp;<a href=\"http:\/\/encodeproject.org\/ENCODE\/\" target=\"_blank\" rel=\"noreferrer noopener\">ENCODE Project<\/a>, the new information is so comprehensive and complex that it has given rise to a new publishing model in which electronic documents and datasets are interconnected.<\/p>\n\n\n\n<p>Just as the&nbsp;<a href=\"http:\/\/www.ornl.gov\/sci\/techresources\/Human_Genome\/project\/about.shtml\" target=\"_blank\" rel=\"noreferrer noopener\">Human Genome Project<\/a>&nbsp;revolutionised biomedical research, ENCODE will drive new understanding and open new avenues for biomedical science. Led by the National Genome Research Institute (<a href=\"http:\/\/www.genome.gov\/\" target=\"_blank\" rel=\"noreferrer noopener\">NHGRI<\/a>) in the US and the EMBL-European Bioinformatics Institute (<a href=\"http:\/\/www.ebi.ac.uk\/Information\/News\/news.html\" target=\"_blank\" rel=\"noreferrer noopener\">EMBL-EBI<\/a>) in the UK, ENCODE now presents a detailed map of genome function that identifies 4 million gene \u2018switches\u2019. This essential reference will help researchers pinpoint very specific areas of research for human disease. The findings are published in 30 connected, open-access papers appearing in three science journals:&nbsp;<em>Nature<\/em>,&nbsp;<em>Genome Biology<\/em>&nbsp;and&nbsp;<em>Genome Research<\/em>.<\/p>\n\n\n\n<p>\u201cOur genome is simply alive with switches: millions of places that determine whether a gene is switched on or off,\u201d says&nbsp;<a href=\"http:\/\/www.ebi.ac.uk\/~birney\" target=\"_blank\" rel=\"noreferrer noopener\">Ewan Birney<\/a>&nbsp;of EMBL-EBI, lead analysis coordinator for ENCODE. \u201cThe Human Genome Project showed that only 2% of the genome contains genes, the instructions to make proteins. With ENCODE, we can see that around<a href=\"http:\/\/dx.doi.org\/10.1038\/nature11247\" target=\"_blank\" rel=\"noreferrer noopener\">&nbsp;80% of the genome is actively doing something<\/a>. We found that a much bigger part of the genome \u2013 a surprising amount, in fact \u2013 is involved in controlling when and where proteins are produced, than in simply manufacturing the building blocks.\u201d<\/p>\n\n\n\n<p>\u201cENCODE data can be used by any disease researcher, whatever pathology they may be interested in,\u201d said Ian Dunham of EMBL-EBI, who played a key role in coordinating the analysis. \u201cIn many cases you may have a good idea of which genes are involved in your disease, but you might not know which switches are involved. Sometimes these switches are very surprising, because their location might seem more logically connected to a completely different disease. ENCODE gives us a set of very valuable leads to follow to discover key mechanisms at play in health and disease. Those can be exploited to create entirely new medicines, or to repurpose existing treatments.\u201d<\/p>\n\n\n\n<p>\u201cENCODE gives us the knowledge we need to look beyond the linear structure of the genome to how the whole network is connected,\u201d commented&nbsp;<a href=\"http:\/\/snyderlab.stanford.edu\/\" target=\"_blank\" rel=\"noreferrer noopener\">Michael Snyder<\/a>, professor and chair at Stanford University and a principal investigator on ENCODE. \u201cWe are beginning to understand the information generated in genome-wide association studies \u2013 not just where certain genes are located, but which sequences control them. Because of the complex, three-dimensional shape of our genome, those controls are sometimes far from the gene they regulate and&nbsp;<a href=\"http:\/\/my5c.umassmed.edu\/about\/about.php\" target=\"_blank\" rel=\"noreferrer noopener\">looping around to make contact<\/a>. Were it not for ENCODE, we might never have looked in those regions. This is a major step toward understanding the wiring diagram of a human being. ENCODE helps us look deeply into the regulatory circuit that tells us how all of the parts come together to make a complex being.\u201d<\/p>\n\n\n\n<p>Until recently, generating and storing large volumes of data has been a challenge in biomedical research. Now, with the falling cost and rising productivity of genome sequencing, the focus has shifted to analysis \u2013 making sense of the data produced in&nbsp;<a href=\"http:\/\/gwas.nih.gov\/\" target=\"_blank\" rel=\"noreferrer noopener\">genome-wide association studies<\/a>. ENCODE partners have been&nbsp;<a href=\"http:\/\/genome.ucsc.edu\/ENCODE\/dataMatrix\/encodeDataMatrixHuman.html\" target=\"_blank\" rel=\"noreferrer noopener\">working systematically<\/a>&nbsp;through the human genome, using the same computational and wet-lab&nbsp;<a href=\"http:\/\/dx.doi.org\/10.1038\/nature11247\" target=\"_blank\" rel=\"noreferrer noopener\">methods and reagents<\/a>&nbsp;in laboratories distributed throughout the world.<\/p>\n\n\n\n<p>To give some sense of the scale of the project: ENCODE combined the efforts of&nbsp;<a href=\"http:\/\/encodeproject.org\/ENCODE\/contributors.html\" target=\"_blank\" rel=\"noreferrer noopener\">442 scientists<\/a>&nbsp;in 32 labs in the UK, US, Spain, Singapore and Japan. They generated and analysed over 15 terabytes (15 trillion bytes) of raw data \u2013 all of which is now publicly available. The study used around 300 years\u2019 worth of computer time studying 147 tissue types to determine what turns specific genes on and off, and how that \u2018switch\u2019 differs between cell types.<\/p>\n\n\n\n<p>The articles published today represent hundreds of pages of research. But the digital publishing group at&nbsp;<em>Nature<\/em>&nbsp;recognises that \u2018pages\u2019 are a thing of the past. All of the published ENCODE content, in all three journals, is connected digitally through topical \u2018threads\u2019, so that readers can follow their area of interest between papers and all the way down to the original data.<\/p>\n\n\n\n<p>\u201cGetting the best people with the best expertise together is what this is all about,\u201d said Ewan Birney. \u201cENCODE has really shown that leading life scientists are very good at collaborating closely on a large scale to produce excellent foundational resources that the whole community can use.\u201d<\/p>\n\n\n\n<p>\u201cUntil now, everyone\u2019s been generating and publishing this data piecemeal and unintentionally trapping it in niche communities and static publications. How could anyone outside that community exploit that knowledge if they don\u2019t know it\u2019s there?\u201d commented&nbsp;<a href=\"http:\/\/big.crg.cat\/bioinformatics_and_genomics\" target=\"_blank\" rel=\"noreferrer noopener\">Roderic Guigo<\/a>&nbsp;of the Centre de Regulaci\u00f3 Gen\u00f3mica (<a href=\"http:\/\/pasteur.crg.es\/portal\/page\/portal\/Internet\/\" target=\"_blank\" rel=\"noreferrer noopener\">CRG<\/a>) in Barcelona, Spain. \u201cWe have now an interactive encyclopaedia that everyone can refer to, and that will make a huge difference.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Today, an international team of researchers reveal that much of what has been called \u2018junk DNA\u2019 in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. Without these switches, genes would not work \u2013 and mutations in these regions&hellip;<\/p>\n","protected":false},"author":16,"featured_media":26172,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[918,1994],"embl_taxonomy":[],"class_list":["post-26170","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-data","tag-encode"],"acf":{"show_featured_image":false,"vf_locked":false,"featured":false,"article_intro":"","article_sources":false,"related_links":false,"in_this_article":false,"color":"#007B53","youtube_url":"","mp4_url":"","video_caption":"","translations":false,"press_contact":"EMBL Generic"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Fast forward for biomedical research | EMBL<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/fast-forward-for-biomedical-research\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Fast forward for biomedical research | EMBL\" \/>\n<meta property=\"og:description\" content=\"Today, an international team of researchers reveal that much of what has been called \u2018junk DNA\u2019 in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. 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