{"id":38452,"date":"2021-06-09T11:20:57","date_gmt":"2021-06-09T09:20:57","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=38452"},"modified":"2024-03-22T11:16:06","modified_gmt":"2024-03-22T10:16:06","slug":"visualising-rna-structures-using-r2dt","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/visualising-rna-structures-using-r2dt\/","title":{"rendered":"Visualising RNA structures using R2DT"},"content":{"rendered":"\n<p>Researchers from <a href=\"https:\/\/www.ebi.ac.uk\/\">EMBL\u2019s European Bioinformatics Institute (EMBL-EBI)<\/a>, <a href=\"https:\/\/www.gatech.edu\/\">Georgia Institute of Technology<\/a>, <a href=\"https:\/\/cuni.cz\/uken-1.html\">Charles University<\/a>, the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/\">National Center for Biotechnology Information<\/a>, the <a href=\"https:\/\/www.ucsc.edu\/\">University of California Santa Cruz, <\/a>and the <a href=\"https:\/\/www.utexas.edu\/\">University of Texas at Austin<\/a> have developed R2DT (RNA 2D Templates), a new user-friendly piece of software for visualising 2D RNA structures.<\/p>\n\n\n\n<p>RNA molecules can be large and complex, and their distinct structure is often crucial for their biological function. A structural hierarchy exists in the architecture of RNA molecules. First, there is the RNA sequence \u2013 the primary structure. The linear RNA molecule can fold to give the RNA its secondary, 2D structure. Within the secondary structure, interactions occur that cause the RNA molecule to adopt a 3D structure.<\/p>\n\n\n\n<p>R2DT provides a new method for visualising 2D RNA structures using a comprehensive framework that extends across many types of RNA, from very small RNA molecules like transfer RNAs to large ribosomal RNAs. Based on a library of 3,632 experimentally validated RNA structures, referred to as templates, R2DT provides consistent and recognisable RNA layouts, openly available to all researchers.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Consistent, reproducible RNA structures<\/h2>\n\n\n\n<p>\u201cResearchers are used to seeing RNA structures in a standard orientation which is widely accepted,\u201d says <a href=\"http:\/\/siret.ms.mff.cuni.cz\/members\/hoksza\/home\">David Hoksza, Assistant Professor at Charles University<\/a>. \u201cFor larger RNAs such as ribosomal RNA this can be tricky, and to tackle this we developed the template-based drawing method implemented within R2DT. Basically, this method takes a template RNA structure and layout and compares this to a new RNA structure of interest to find commonalities between the two structures.\u201d<\/p>\n\n\n\n<p>R2DT has been extensively tested on over 13 million RNA sequences from the <a href=\"https:\/\/rnacentral.org\/\">RNAcentral<\/a> resource, to ensure that the 2D RNA structures it generates are consistent and reproducible. The R2DT framework can also be easily updated and extended with new RNA structures including newly identified viral RNAs. The software is freely available through <a href=\"https:\/\/github.com\/rnacentral\/R2DT\">GitHub<\/a> and <a href=\"https:\/\/rnacentral.org\/r2dt\">RNAcentral<\/a>.&nbsp;<\/p>\n\n\n\n<p>\u201cIt\u2019s important for researchers to visualise RNA structures in a layout that they will be familiar with,\u201d says <a href=\"https:\/\/www.ebi.ac.uk\/about\/people\/anton-petrov\">Anton I. Petrov, Project Leader at EMBL-EBI<\/a>. \u201cFor decades, researchers have been visualising RNA structures in a way that provides clear meaning to the various parts of the diagrams. This is what we can now produce automatically at a massive scale using R2DT.\u201d<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">3D information in a 2D structure<\/h2>\n\n\n\n<p>The interactions within an RNA structure can be represented in a 2D diagram, used by scientists to investigate the function of RNAs. These 2D diagrams are preferred by researchers as they\u2019re far more accessible and can present a broader variety of information than the corresponding 3D structures. R2DT uses experimentally determined 3D structures and feeds this information into the 2D diagrams to improve the traditional 2D RNA layouts.<\/p>\n\n\n\n<p>\u201cThis software allows us to map complex information from 3D RNA structures into a 2D structure which can be visualised much more easily,&#8221; says <a href=\"https:\/\/cool.gatech.edu\/people\/petrov-anton\">Anton S. Petrov, Co-Investigator at Georgia Institute of Technology<\/a>. \u201cYou could say that these secondary structures are similar to the information we receive from Google Maps; a flat projection of 3D structures but retaining all the vital information.\u201d<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Help from the public<\/h2>\n\n\n\n<p>The <a href=\"https:\/\/rfam.org\/\">Rfam<\/a> resource contains data on different RNA families, which are made up of individual RNA molecules with similar structures and sequences. To help explain this idea to a lay audience, Anton I. Petrov and colleagues developed an award-winning public engagement activity called <a href=\"https:\/\/www.youtube.com\/watch?v=gKi3vWgt-UU&amp;t=2s&amp;ab_channel=WellcomeConnectingSciencePublicEngagement\">Genome Explorers<\/a>. This activity gets participants to sort different RNAs by their shapes \u2013 their secondary structures generated by R2DT \u2013 and put those that look alike into groups.<\/p>\n\n\n\n<p>Watching people sort the RNA structures in this way made it clear to the researchers that the structures needed to be orientated in the same way to allow participants to compare them easily. This gave them several ideas for improving the R2DT algorithm to ensure that RNA structures are generated in the same orientation. They have now deployed this new feature within R2DT, RNAcentral, and Rfam.<\/p>\n\n\n\n<p><strong>Find out more<\/strong><\/p>\n\n\n\n<p><a href=\"https:\/\/www.ebi.ac.uk\/about\/public-engagement\/case-studies\/rfam\/\">Learn more about the Genome Explorers activity<\/a><\/p>\n\n\n\n<p>This post was originally published on <a href=\"https:\/\/www.ebi.ac.uk\/about\/news\/announcements\/visualising-rna-structures-using-r2dt\" data-href=\"insert original\" rel=\"canonical nofollow noopener noreferrer\" target=\"_blank\">EMBL-EBI News<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>New software enables scientists to visualise RNA secondary structures using the world\u2019s largest RNA structure dataset.<\/p>\n","protected":false},"author":77,"featured_media":38456,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[918,1772,782,36,861,70],"embl_taxonomy":[2906],"class_list":["post-38452","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-data","tag-data-service","tag-database","tag-embl-ebi","tag-public-engagement","tag-rna","embl_taxonomy-embl-ebi"],"acf":{"featured":true,"show_featured_image":false,"color":"#007B53","link_color":"#fff","article_intro":"<p>New software enables scientists to visualise RNA secondary structures using the world\u2019s largest RNA structure dataset<\/p>\n","related_links":[{"link_description":"","link_url":""},{"link_description":"","link_url":""},{"link_description":"","link_url":""}],"article_sources":[{"source_description":"<p>Sweeney, B.A., <em>et al<\/em>. R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types. <em>Nature Communi<\/em><em>cations<\/em>. Published on 09 June 2021. DOI:10.1038\/s41467-021-23555-5<\/p>\n","source_link_url":"https:\/\/www.nature.com\/articles\/s41467-021-23555-5"}],"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","press_contact":"None","vf_locked":false,"field_target_display":"embl","source_article":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"a99d1a7c-ca83-4c00-ab61-d082d3e41ce3\";}","parents":[],"name":["EMBL-EBI"],"slug":"embl-ebi","description":"Where &gt; All EMBL sites &gt; EMBL-EBI"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Visualising RNA structures using R2DT | EMBL<\/title>\n<meta name=\"description\" content=\"New software enables scientists to visualise RNA secondary structures using the world\u2019s largest RNA structure dataset.\" \/>\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\/visualising-rna-structures-using-r2dt\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Visualising RNA structures using R2DT | EMBL\" \/>\n<meta property=\"og:description\" content=\"New software enables scientists to visualise RNA secondary structures using the world\u2019s largest RNA structure dataset.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/visualising-rna-structures-using-r2dt\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2021-06-09T09:20:57+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-03-22T10:16:06+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2021\/05\/2021_PETROV_R2DT_1000x600.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"600\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Vicky Hatch\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@embl\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Vicky Hatch\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/visualising-rna-structures-using-r2dt\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/visualising-rna-structures-using-r2dt\/\"},\"author\":{\"name\":\"Vicky Hatch\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/d8477ba2d7a6164b141a3872a25ee982\"},\"headline\":\"Visualising RNA structures using R2DT\",\"datePublished\":\"2021-06-09T09:20:57+00:00\",\"dateModified\":\"2024-03-22T10:16:06+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/visualising-rna-structures-using-r2dt\/\"},\"wordCount\":683,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/visualising-rna-structures-using-r2dt\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2021\/05\/2021_PETROV_R2DT_1000x600.jpg\",\"keywords\":[\"data\",\"data service\",\"database\",\"embl-ebi\",\"public engagement\",\"rna\"],\"articleSection\":[\"Science\",\"Science &amp; 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