All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies

<!DOCTYPE html> <html lang="en" > <head itemscope itemtype="http://schema.org/WebPage" prefix="og: http://ogp.me/ns#" > <meta charset="UTF-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge">  <meta name="HandheldFriendly" content="True"> <meta name="MobileOptimized" content="320"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <link rel="preconnect" href="https://cdn.ncbi.nlm.nih.gov"> <link rel="preconnect" href="https://www.ncbi.nlm.nih.gov"> <link rel="preconnect" href="https://www.google-analytics.com"> <link rel="stylesheet" href="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/CACHE/css/output.5ecf62baa0fa.css" type="text/css"> <link rel="stylesheet" href="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/CACHE/css/output.452c70ce66f7.css" type="text/css"> <link rel="stylesheet" href="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/CACHE/css/output.7bf600913d6e.css" type="text/css"> <link rel="stylesheet" href="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/CACHE/css/output.0bfa59184c7a.css" type="text/css"> <title>All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies - PubMed</title> <link rel="preload" as="font" href="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/uswds/dist/fonts/merriweather-bold-webfont.woff2" type="font/woff2" crossorigin />  <link rel="shortcut icon" type="image/ico" href="https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.ico" /> <link rel="icon" type="image/png" href="https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon.png" />  <link rel="icon" type="image/png" sizes="192x192" href="https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-192.png" />  <link rel="apple-touch-icon-precomposed" href="https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-57.png">  <link rel="apple-touch-icon-precomposed" sizes="72x72" href="https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-72.png">  <link rel="apple-touch-icon-precomposed" sizes="114x114" href="https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-114.png">  <link rel="apple-touch-icon-precomposed" sizes="144x144" href="https://cdn.ncbi.nlm.nih.gov/coreutils/nwds/img/favicons/favicon-144.png">  <meta name="ncbi_sg_optimize_id" content="">  <meta name="theme-color" content="#20558a">  <meta name="referrer" content="origin-when-cross-origin"> <meta name="ncbi_pinger_gtm_track" content="true"/>  <meta name="ncbi_app" content="pubmed" /> <meta name="ncbi_db" content="pubmed" /> <meta name="ncbi_phid" content="3C3A00019EBA731500003493A2E5F2CD.1.m_7" /> <meta name="ncbi_pinger_stat_url" content="https://www.ncbi.nlm.nih.gov/stat" /> <meta name="log_category" content="literature" /> <meta name="ncbi_cost_center" content="pubmed" />  <meta name="ncbi_pdid" content="abstract" /> <meta name="log_op" content="retrieve" /> <meta name="uid" content="39433914" /> <meta name="ncbi_uid" content="39433914" /> <meta name="log_displayeduids" content="39433914" /> <meta name="log_source_db" content="pubmed" /> <meta name="log_icons_present" content="true" />  <meta name="description" content="RNA modifications are essential for human health - too much or too little of them leads to serious illnesses ranging from neurodevelopmental disorders to cancer. Technical advances in RNA modification sequencing are beginning to uncover the RNA targets of diverse RNA-modifying enzymes that are dysre …"><meta name="keywords" content="pmid:39433914, doi:10.1038/s41580-024-00784-2, Review, Shalini Oberdoerffer, Wendy V Gilbert, PubMed Abstract, NIH, NLM, NCBI, National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine, MEDLINE"><meta name="robots" content="index,nofollow,noarchive"><meta property="og:title" content="All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies - PubMed"><meta property="og:url" content="https://pubmed.ncbi.nlm.nih.gov/39433914/"><meta property="og:description" content="RNA modifications are essential for human health - too much or too little of them leads to serious illnesses ranging from neurodevelopmental disorders to cancer. Technical advances in RNA modification sequencing are beginning to uncover the RNA targets of diverse RNA-modifying enzymes that are dysre …"><meta property="og:image" content="https://cdn.ncbi.nlm.nih.gov/pubmed/persistent/pubmed-meta-image-v2.jpg"><meta property="og:image:secure_url" content="https://cdn.ncbi.nlm.nih.gov/pubmed/persistent/pubmed-meta-image-v2.jpg"><meta property="og:type" content="website"><meta property="og:site_name" content="PubMed"><meta name="twitter:domain" content="pubmed.ncbi.nlm.nih.gov"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:title" content="All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies - PubMed"><meta name="twitter:url" content="https://pubmed.ncbi.nlm.nih.gov/39433914/"><meta name="twitter:description" content="RNA modifications are essential for human health - too much or too little of them leads to serious illnesses ranging from neurodevelopmental disorders to cancer. Technical advances in RNA modification sequencing are beginning to uncover the RNA targets of diverse RNA-modifying enzymes that are dysre …"><meta name="twitter:image" content="https://cdn.ncbi.nlm.nih.gov/pubmed/persistent/pubmed-meta-image-v2.jpg">  <link rel="search" type="application/opensearchdescription+xml" href="https://cdn.ncbi.nlm.nih.gov/pubmed/persistent/opensearch.xml" title="PubMed search">  <noscript> <link rel="stylesheet" type="text/css" href="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/core/no-script.css"> </noscript> <meta name="citation_title" content="All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies"> <meta name="citation_authors" content="Oberdoerffer S;Gilbert WV;"> <meta name="citation_date" content="10/21/2024"> <meta name="citation_publisher" content="Nat Rev Mol Cell Biol"> <meta name="citation_journal_title" content="Nature reviews. Molecular cell biology"> <meta name="citation_pmid" content="39433914"> <meta name="citation_abstract_html_url" content="https://pubmed.ncbi.nlm.nih.gov/39433914/"> <meta name="citation_doi" content="10.1038/s41580-024-00784-2"> <meta name="citation_issn" content="1471-0080"> <link rel="canonical" href="https://pubmed.ncbi.nlm.nih.gov/39433914/" /> </head> <body > <noscript> <div class="no-script-banner" id="no-script-banner"> <div class="warning-message"> <div class="warning-message-text"> This site needs JavaScript to work properly. Please enable it to take advantage of the complete set of features! </div> </div> </div> </noscript> <div class="no-session-banner" id="no-session-banner" hidden> <div class="warning-message"> <div class="warning-message-text"> Clipboard, Search History, and several other advanced features are temporarily unavailable. </div> <button class="close-banner-button" title="Close Clipboard and Search History not available warning banner" ref="linksrc=close_no_session_banner" aria-controls="no-session-banner" aria-label="Close Clipboard and Search History not available warning banner" aria-expanded="true"> </button> </div> </div> <a class="usa-skipnav" href="#article-details"> Skip to main page content </a>  <section class="usa-banner"> <div class="usa-accordion"> <header class="usa-banner-header"> <div class="usa-grid usa-banner-inner"> <img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" /> <p>An official website of the United States government</p> <button class="usa-accordion-button usa-banner-button" aria-expanded="false" aria-controls="gov-banner-top" > <span class="usa-banner-button-text">Here's how you know</span> </button> </div> </header> <div class="usa-banner-content usa-grid usa-accordion-content" id="gov-banner-top" > <div class="usa-banner-guidance-gov usa-width-one-half"> <img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-dot-gov.svg" alt="Dot gov" /> <div class="usa-media_block-body"> <p> <strong>The .gov means it’s official.</strong> <br /> Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site. </p> </div> </div> <div class="usa-banner-guidance-ssl usa-width-one-half"> <img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg" alt="Https" /> <div class="usa-media_block-body"> <p> <strong>The site is secure.</strong> <br /> The <strong>https://</strong> ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely. </p> </div> </div> </div> </div> </section> <div class="usa-overlay"></div> <header class="ncbi-header" role="banner" data-section="Header"> <div class="usa-grid"> <div class="usa-width-one-whole"> <div class="ncbi-header__logo"> <a href="https://www.ncbi.nlm.nih.gov/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo"> <img src="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg" alt="NIH NLM Logo" /> </a> </div> <div class="ncbi-header__account"> <a id="account_login" href="https://account.ncbi.nlm.nih.gov" class="usa-button header-button" style="display:none" data-ga-action="open_menu" data-ga-label="account_menu">Log in</a> <button id="account_info" class="header-button" style="display:none" aria-controls="account_popup"> <span class="fa fa-user" aria-hidden="true"></span> <span class="username desktop-only" aria-hidden="true" id="uname_short"></span> <span class="sr-only">Show account info</span> </button> </div> <div class="ncbi-popup-anchor"> <div class="ncbi-popup account-popup" id="account_popup" aria-hidden="true"> <div class="ncbi-popup-head"> <button class="ncbi-close-button" data-ga-action="close_menu" data-ga-label="account_menu"><span class="fa fa-times"></span><span class="usa-sr-only">Close</span></button> <h4>Account</h4> </div> <div class="account-user-info"> Logged in as:<br/> <b><span class="username" id="uname_long">username</span></b> </div> <div class="account-links"> <ul class="usa-unstyled-list"> <li><a id="account_myncbi" href="/myncbi/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_myncbi">Dashboard</a></li> <li><a id="account_pubs" href="/myncbi/collections/bibliography/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_pubs">Publications</a></li> <li><a id="account_settings" href="/account/settings/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_settings">Account settings</a></li> <li><a id="account_logout" href="/account/signout/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_logout">Log out</a></li> </ul> </div> </div> </div> </div> </div> </header> <div role="navigation" aria-label="access keys"> <a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a> <a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a> <a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a> <a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a> <a id="nws_header_accesskey_4" href="#" class="usa-sr-only" accesskey="4" tabindex="-1">Main Navigation</a> </div> <section data-section="Alerts"> <div class="ncbi-alerts-placeholder"></div> </section>  <a id="maincontent" aria-label="Main page content below" role="navigation"></a> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <form action="/" method="get" autocomplete="off" class="usa-search usa-search-big search-form content-page-layout" id="search-form" role="search"> <div class="inner-wrap"> <a class="pubmed-logo" aria-label="Pubmed Logo" href="/" data-ga-category="featured_link" data-ga-action="pubmed_logo"> <img src="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/core/images/pubmed-logo-blue.svg" alt="pubmed logo" /> </a> <a href="#" class="search-input-trigger" data-alt-title="Hide search bar" title="Show search bar" aria-label="Show search bar"> </a> <div role="search" class="search-input"> <div class="form-field "> <label class="usa-sr-only" for="id_term"> Search: </label> <input type="search" name="term" data-skip-ie-scroll-to-top="" data-replace-term-with-exact="" data-exact-query="" placeholder="" class="term-input" required="required" id="id_term"/><a href="#" class="clear-btn" aria-label="Clear search input" title="Clear search input" role="button" data-pinger-ignore></a><button type="submit" class="search-btn" aria-label="Search" disabled data-pinger-ignore><span class="usa-search-submit-text">Search</span></button> </div> </div>   <div class="search-links-wrapper content-page-layout"> <div class="search-links"> <a href="/advanced/" class="search-input-link adv-search-link" data-ga-category="featured_link" data-ga-action="adv_search">Advanced</a> <a href="/clipboard/" class="search-input-link clipboard-link hidden" data-ga-category="featured_link" data-ga-action="clipboard"> Clipboard <span class="amount-in-clipboard"></span> </a> </div> <span class="search-input-link user-guide-link" role="navigation" aria-label="User guide"> <a href="/help/" data-ga-category="featured_link" data-ga-action="user_guide"> User Guide </a> </span> </div> </div> </form> <div id="article-page-header"> <div id="article-top-actions-bar" class="article-top-actions-bar"> <div class="inner-wrap"> <div class="actions-container"> <div class="return-to-search"> </div> <div class="multiple-results-actions " role="region" aria-label="save, email, send to"> <button id="save-results-panel-trigger" type="button" class="save-results save-results-panel-trigger" aria-expanded="false" aria-controls="save-action-panel" data-ga-category="save_share" data-ga-action="save" data-ga-label="open"> Save </button><button id="email-results-panel-trigger" type="button" class="email-results email-results-panel-trigger" aria-expanded="false" aria-controls="email-action-panel" data-ga-category="save_share" data-ga-action="email" data-ga-label="open"> Email </button><div class="more-actions dropdown-block"><button id="more-actions-trigger" type="button" class="trigger more-actions-trigger" ref="linksrc=show_moreactions_btn" aria-label="Send to" aria-controls="more-actions-dropdown">Send to</button><div id="more-actions-dropdown" class="dropdown dropdown-container" hidden><div class="content"><ul class="more-actions-links"><li><a class="clipboard-panel-trigger dropdown-block-link " href="#" role="button" data-ga-category="save_share" data-ga-action="clipboard" data-ga-label="send"> Clipboard </a></li><li><a role="button" class="dropdown-block-link bibliography-trigger-target" href="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39433914%2F%23open-bibliography-panel">My Bibliography</a></li><li><a role="button" class="dropdown-block-link collections-trigger-target" href="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39433914%2F%23open-collections-panel">Collections</a></li><li><a role="button" class="citation-manager-panel-trigger dropdown-block-link citation-manager-trigger-target" href="#">Citation manager</a></li></ul></div></div></div> </div> <div class="display-options" data-format-key="format" data-default-format-value="abstract" data-current-format-value="abstract" role="region"> <button class="trigger usa-button" title="Change format" data-ga-category="display_options" data-ga-action="display_options_dialog"> <span class="button-label">Display options</span> </button> <div class="dropdown" hidden> <div class="title"> Display options </div> <div class="content"> <div class="format-container"> <span class="option-label"> Format </span> <select name="format" data-initial-value="abstract" aria-label="Display format" id="article-display-format"> <option value="abstract">Abstract</option> <option value="pubmed">PubMed</option> <option value="pmid">PMID</option> </select> </div> </div> </div> </div> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> </div> </div> </div> <div id="article-panels-container" class="article-panels-container"> <div id="save-action-panel" class="save-action-panel action-panel" aria-hidden="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Save citation to file </h2> <form id="save-action-panel-form" class="action-panel-content action-form" action="/results-export-ids/" data-by-search-action="/results-export-search-data/" data-by-ids-action="/results-export-ids/" method="post" data-by-search-method="post" data-by-ids-method="post"> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <div class="action-panel-control-wrap"> <label for="save-action-format" class="action-panel-label"> Format: </label> <select id="save-action-format" name="results-format" class="action-panel-selector"> <option value="summary-text">Summary (text)</option> <option value="pubmed-text">PubMed</option> <option value="pmid">PMID</option> <option value="abstract">Abstract (text)</option> <option value="csv">CSV</option> </select> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Saving..." data-ga-category="save_share" data-ga-action="save" data-ga-label="save"> Create file </button> <button class="action-panel-cancel" aria-label="Close 'Save citations to file' panel" ref="linksrc=close_save_panel" aria-controls="save-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="save" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="email-action-panel" class="email-action-panel action-panel" aria-hidden="true" data-recaptcha-script-url="https://www.recaptcha.net/recaptcha/enterprise.js?render=explicit&onload=onloadCaptchaCallback" data-recaptcha-enabled="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Email citation </h2> <form id="email-action-panel-form" class="action-panel-content action-form" action="/send-email/" data-by-search-action="/results-export-email-by-search-data/" data-by-ids-action="/send-email/" data-by-search-method="post" data-by-ids-method="post" method="post" > <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <div class="action-panel-control-wrap"> <span class="action-panel-label"> Subject: </span> <span class="email-subject" id="email-subject" aria-label="Email subject">1 selected item: 39433914 - PubMed</span> <input type="hidden" name="email-subject" value="1 selected item: 39433914"/> <input type="hidden" name="email-subject-hash" value="cc69cb98351661b0da24dae4ff47a9f44d7850066057064433b80c8d08c6db05"/> </div> <div class="action-panel-control-wrap"> <label for="email-to" class="action-panel-label required-field-asterisk"> To: </label> <input type="email" aria-label="Recipient Email Address" placeholder="email@example.com" id="email-to" class="email-to" pattern="^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$" maxlength="100" required> </div> <div class="action-panel-control-wrap"> <label for="email-from" class="action-panel-label"> From: </label> <input type="email" aria-label="Sender Email Address" placeholder="email@example.com" id="email-from" class="email-from" pattern="^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$" maxlength="256"> </div> <div class="action-panel-control-wrap"> <label for="email-citation-format" class="action-panel-label"> Format: </label> <select id="email-citation-format" name="citation-format" class="action-panel-selector email-citation-format"> <option selected="selected" value="summary">Summary</option> <option value="summary-text">Summary (text)</option> <option value="abstract">Abstract</option> <option value="abstract-text">Abstract (text)</option> </select> </div> <div class="include-supplemental-container"> <input type="checkbox" aria-label="Include MeSH and other data" name="include-supplemental" id="email-include-supplemental" class="email-include-supplemental"> <label for="email-include-supplemental" class="email-include-supplemental-label">MeSH and other data</label> </div> <div class="form-field recaptcha "> <div class="g-recaptcha" id="id-recaptcha" data-sitekey="6LfsWHMdAAAAAClKbtOpjQ2pMjgsGxvv7NdZW9uI"></div> </div> <div id="captcha-error-message" class="usa-input-error-message captcha-validation-message" role="alert"></div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Sending..." data-ga-category="save_share" data-ga-action="email" data-ga-label="send"> Send email </button> <button class="action-panel-cancel" aria-label="Close 'Email citations' panel" ref="linksrc=close_email_panel" aria-controls="email-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="email" data-ga-label="cancel"> Cancel </button> </div> <input type="hidden" name="email-search-details" value="" /> <input type="hidden" name="email-search-details-hash" value="0e42663a6c3bd85498fcb88798998fed7bfdc45d457db35281e41afe13cc0524" /> </form> </div> </div> <div id="collections-action-panel" class="collections-action-panel action-panel in-progress-dots-panel" aria-hidden="true" data-collections-open-panel-enabled="false" data-collections-open-panel-url-hash="#open-collections-panel"> <div class="inner-wrap"> <h3 class="action-panel-heading"> Add to Collections </h3> <form id="collections-action-panel-form" class="collections-action-panel-form action-panel-content action-form action-panel-smaller-selectors" data-existing-collections-url="/list-existing-collections/" data-add-to-existing-collection-url="/add-to-existing-collection/" data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/" data-get-article-ids-by-search-url="/get-article-ids-by-search/" data-myncbi-max-collection-name-length="100" data-add-to-collection-max-amount="1000" data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/"> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <div class="choice-group" role="radiogroup"> <ul class="radio-group-items"> <li> <input type="radio" id="collections-action-panel-new" class="collections-new" name="collections" value="new" data-ga-category="save_share" data-ga-action="collections" data-ga-label="collections_radio_new"> <label for="collections-action-panel-new">Create a new collection</label> </li> <li> <input type="radio" id="collections-action-panel-existing" class="collections-existing" name="collections" value="existing" checked="true" data-ga-category="save_share" data-ga-action="collections" data-ga-label="collections_radio_existing"> <label for="collections-action-panel-existing">Add to an existing collection</label> </li> </ul> </div> <div class="controls-wrapper"> <div class="action-panel-control-wrap new-collections-controls"> <label for="collections-action-panel-add-to-new" class="action-panel-label required-field-asterisk"> Name your collection: </label> <input type="text" name="add-to-new-collection" id="collections-action-panel-add-to-new" class="collections-action-add-to-new" pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/" maxlength="100" data-ga-category="save_share" data-ga-action="create_collection" data-ga-label="non_favorties_collection"> <div class="collections-new-name-too-long usa-input-error-message selection-validation-message"> Name must be less than 100 characters </div> </div> <div class="action-panel-control-wrap existing-collections-controls"> <label for="collections-action-panel-add-to-existing" class="action-panel-label"> Choose a collection: </label> <select id="collections-action-panel-add-to-existing" class="action-panel-selector collections-action-add-to-existing" data-ga-category="save_share" data-ga-action="select_collection" data-ga-label="($('#collections-action-add-to-existing').val() === 'Favorites') ? 'Favorites' : 'non_favorites_collection'"> </select> <div class="collections-retry-load-on-error usa-input-error-message selection-validation-message"> Unable to load your collection due to an error<br> <a href="#">Please try again</a> </div> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Adding..." data-pinger-ignore data-ga-category="save_share" data-ga-action="collections" data-ga-label="add"> Add </button> <button class="action-panel-cancel" aria-label="Close 'Add to Collections' panel" ref="linksrc=close_collections_panel" aria-controls="collections-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="collections" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="bibliography-action-panel" class="bibliography-action-panel action-panel in-progress-dots-panel" aria-hidden="true" data-bibliography-open-panel-enabled="false" data-bibliography-open-panel-url-hash="#open-bibliography-panel"> <div class="inner-wrap"> <h3 class="action-panel-heading"> Add to My Bibliography </h3> <form id="bibliography-action-panel-form" class="bibliography-action-panel-form action-panel-content action-form action-panel-smaller-selectors" data-add-to-bibliography-max-amount="100" data-add-to-bibliography-batch-size="10" data-bibliography-delegates-url="/list-bibliography-delegates/" data-add-to-bibliography-url="/add-to-bibliography/" data-get-article-ids-by-search-url="/get-article-ids-by-search/" data-mybib-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/mybibliography/"> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <div class="action-panel-control-wrap bibliographies-controls"> <div class="choice-group"> <ul class="bibliographies-action-add radio-group-items"> <li> <input name="bibliography" id="my-bibliography" class="my-bibliography" type="radio" checked/> <label for="my-bibliography">My Bibliography</label> </li> </ul> </div> </div> <div class="bibliographies-retry-load-on-error usa-input-error-message selection-validation-message"> Unable to load your delegates due to an error<br> <a href="#">Please try again</a> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Adding..." data-pinger-ignore> Add </button> <button class="action-panel-cancel" aria-label="Close 'Add to bibliography' panel" ref="linksrc=close_bibliography_panel" aria-controls="bibliography-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="mybib" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="saved-search-action-panel" class="saved-search-action-panel action-panel " aria-hidden="true" data-saved-search-open-panel-enabled="false" data-saved-search-open-panel-url-hash="#open-saved-search-panel"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Your saved search </h2> <form id="saved-search-action-panel-form" class="saved-search-action-panel-form action-panel-content action-form" data-create-saved-search-url="/create-saved-search/" data-try-search-terms-url="/try-search-term/" data-saved-search-root-url="https://www.ncbi.nlm.nih.gov/myncbi/searches/"> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <div class="action-panel-control-wrap"> <label for="saved-search-name" class="action-panel-label saved-search-name-label required-field-asterisk"> Name of saved search: </label> <input maxlength="200" type="text" name="saved-search-name" id="saved-search-name" class="saved-search-name" value="" required pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"> </div> <div class="action-panel-control-wrap"> <label for="saved-search-term" class="action-panel-label required-field-asterisk"> Search terms: </label> <textarea name="saved-search-term" id="saved-search-term" class="saved-search-term" required></textarea> </div> <div class="test-search-term-wrap"> <a href="#" class="try-search-term">Test search terms</a> </div> <div class="choice-group action-panel-extra-margin-top"> <span class="action-panel-label" id="fieldset-label"> Would you like email updates of new search results? </span> <fieldset id="saved-search-alert" aria-describedby="fieldset-label"> <legend class="usa-sr-only">Saved Search Alert Radio Buttons</legend> <ul class="radio-group-items"> <li> <input type="radio" id="saved-search-alert-yes" class="saved-search-alert-yes" name="saved-search-alert" value="yes" checked> <label for="saved-search-alert-yes" class="action-panel-label">Yes</label> </li> <li> <input aria-label="No radio input" type="radio" id="saved-search-alert-no" class="saved-search-alert-no" name="saved-search-alert" value="no"> <label for="saved-search-alert-no" class="action-panel-label">No</label> </li> </ul> </fieldset> </div> <div class="alert-schedule-wrap"> <div class="action-panel-control-wrap"> <label class="action-panel-label"> Email: </label> <span aria-label="Email address" id="saved-search-email" class="action-panel-label"><span class="action-panel-label-bold"></span> (<a class="myncbi-account-settings" href="https://www.ncbi.nlm.nih.gov/account/settings/">change</a>)</span> </div> <div class="action-panel-control-wrap action-panel-extra-margin-top"> <label for="saved-search-frequency" class="action-panel-label"> Frequency: </label> <select id="saved-search-frequency" class="no-border-panel-selector saved-search-frequency"> <option value="monthly">Monthly</option> <option value="weekly">Weekly</option> <option value="daily">Daily</option> </select> </div> <div class="action-panel-control-wrap saved-search-monthly-additional"> <label for="saved-search-monthly-on-day" class="action-panel-label"> Which day? </label> <select id="saved-search-monthly-on-day" class="no-border-panel-selector"> <option value="Sunday">The first Sunday</option> <option value="Monday">The first Monday</option> <option value="Tuesday">The first Tuesday</option> <option value="Wednesday">The first Wednesday</option> <option value="Thursday">The first Thursday</option> <option value="Friday">The first Friday</option> <option value="Saturday">The first Saturday</option> <option value="day">The first day</option> <option value="weekday">The first weekday</option> </select> </div> <div class="action-panel-control-wrap saved-search-weekly-additional"> <label for="saved-search-weekly-on-day" class="action-panel-label"> Which day? </label> <select id="saved-search-weekly-on-day" class="no-border-panel-selector saved-search-weekly-on-day"> <option value="Sunday">Sunday</option> <option value="Monday">Monday</option> <option value="Tuesday">Tuesday</option> <option value="Wednesday">Wednesday</option> <option value="Thursday">Thursday</option> <option value="Friday">Friday</option> <option value="Saturday">Saturday</option> </select> </div> <div class="action-panel-control-wrap"> <label for="saved-search-report" class="action-panel-label"> Report format: </label> <select id="saved-search-report" class="no-border-panel-selector saved-search-report"> <option value="DocSum">Summary</option> <option value="DocSumText">Summary (text)</option> <option value="Abstract">Abstract</option> <option value="AbstractText">Abstract (text)</option> <option value="MEDLINE">PubMed</option> </select> </div> <div class="action-panel-control-wrap"> <label for="saved-search-amount" class="action-panel-label"> Send at most: </label> <select id="saved-search-amount" class="no-border-panel-selector saved-search-amount"> <option value="1">1 item</option> <option value="5" selected>5 items</option> <option value="10">10 items</option> <option value="20">20 items</option> <option value="50">50 items</option> <option value="100">100 items</option> <option value="200">200 items</option> </select> </div> <div> <input type="checkbox" id="saved-search-send-if-no-result" class="saved-search-send-if-no-result" name="saved-search-send-if-no-result"> <label for="saved-search-send-if-no-result" class="action-panel-label smaller-checkbox"> Send even when there aren't any new results </label> </div> <div class="action-panel-control-wrap option-text-in-email-wrap"> <label for="saved-search-email-text" class="action-panel-label"> Optional text in email: </label> <textarea name="saved-search-email-text" id="saved-search-email-text" class="saved-search-email-text"></textarea> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Saving..." data-ga-category="save_share" data-ga-action="alert" data-ga-label="save"> Save </button> <button class="action-panel-cancel" aria-label="Close 'Your saved search' panel" ref="linksrc=close_saved_search_panel" aria-controls="saved-search-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="alert" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="citation-manager-action-panel" class="citation-manager-action-panel action-panel" aria-hidden="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Create a file for external citation management software </h2> <form id="citation-manager-action-panel-form" class="action-panel-content action-form" action="/results-export-ids/" data-by-search-action="/results-export-search-data/" data-by-ids-action="/results-export-ids/" method="post" data-by-search-method="post" data-by-ids-method="post"> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <input name="results-format" type="hidden" value="pubmed"/> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Sending..." data-ga-category="save_share" data-ga-action="citation_manager" data-ga-label="save"> Create file </button> <button class="action-panel-cancel" aria-label="Close 'Send citations to citation manager' panel" ref="linksrc=close_citation_manager_panel" aria-controls="citation-manager-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="citation_manager" data-ga-label="cancel"> Cancel </button> </div> </form> </div> </div> <div id="rss-action-panel" class="rss-action-panel action-panel " aria-hidden="true"> <div class="inner-wrap"> <h2 class="action-panel-heading"> Your RSS Feed </h2> <form id="rss-action-panel-form" class="rss-action-panel-form action-panel-content action-form" data-create-rss-feed-url="/create-rss-feed-url/" data-search-form-term-value=""> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <div class="action-panel-control-wrap"> <label for="rss-name" class="action-panel-label required-field-asterisk"> Name of RSS Feed: </label> <input maxlength="200" placeholder="Name" type="text" name="rss-name" id="rss-name" class="rss-name" value='' required pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/"> </div> <div class="rss-limit-wrap"> <div class="action-panel-control-wrap action-panel-extra-margin-top"> <label for="rss-limit" class="action-panel-label"> Number of items displayed: </label> <select id="rss-limit" class="no-border-panel-selector rss-limit"> <option value="5">5</option> <option value="10">10</option> <option value="15" selected="selected">15</option> <option value="20">20</option> <option value="50">50</option> <option value="100">100</option> </select> </div> </div> <div class="action-panel-actions"> <button class="action-panel-submit" type="submit" data-loading-label="Creating..." data-ga-category="save_share" data-ga-action="alert" data-ga-label="save"> Create RSS </button> <button class="action-panel-cancel" aria-label="Close 'Your RSS' panel" ref="linksrc=close_rss_panel" aria-controls="rss-action-panel" aria-expanded="false" data-ga-category="save_share" data-ga-action="alert" data-ga-label="cancel"> Cancel </button> </div> <div class="action-panel-control-wrap rss-link-copy-wrap"> <label for="rss-link" class="usa-sr-only">RSS Link</label> <input placeholder="Your RSS Feed Link" type="text" name="rss-link" id="rss-link" class="rss-link" title="RSS Link"> <button type="button" disabled class="rss-link-copy-button disabled" data-ga-category="save_share" data-ga-action="rss" data-ga-label="copy"> Copy </button> </div> </form> </div> </div> </div> </div> <div class="article-page" id="article-page" data-article-pmid="39433914"> <aside class="page-sidebar"> <div class="inner-wrap"> <div class="full-text-links"> <div class="full-view"> <h3 class="title"> Full text links </h3> <div class="full-text-links-list"> <a class="link-item dialog-focus" href="https://doi.org/10.1038/s41580-024-00784-2" target="_blank" rel="noopener" ref="linksrc=fulltextorjournal_fulltext&is_pmc=False&PrId=3094&itool=Abstract-def&log$=linkouticon&uid=39433914&db=pubmed&nlmid=100962782" title="See full text options at Nature Publishing Group" data-ga-category="full_text" data-ga-action="Nature Publishing Group" data-ga-label="39433914" ><img src="https://cdn.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--www.nature.com-static-images-logos-nature-portfolio-120.png" alt="full text provider logo"><span class="text"> Nature Publishing Group </span></a> </div> </div> <div class="short-view"> <a href="#" class="full-text-links-button full-text-links-dialog-trigger"> Full text links </a> </div> </div> <div class="actions-buttons sidebar"><h3 class="title">Actions</h3><div class="inner-wrap"><button class="citation-button citation-dialog-trigger" aria-label="Open dialog with citation text in different styles" data-ga-category="save_share" data-ga-action="cite" data-ga-label="open" data-all-citations-url="/39433914/citations/" data-citation-style="nlm" data-pubmed-format-link="/39433914/export/"><span class="button-label">Cite</span></button><link type="text/css" href="ncbi-overlay-block/src/overlay-block.css"><div class="collections-button-container" data-article-id="39433914" data-article-db="pubmed"><button class="collections-button collections-dialog-trigger" aria-label="Save article in MyNCBI collections." data-ga-category="collections_button" data-ga-action="click" data-ga-label="collections_button" data-collections-open-dialog-enabled="false" data-collections-open-dialog-url="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39433914%2F%23open-collections-dialog" data-in-collections="false"><span class="button-label">Collections</span></button><div class="overlay" role="dialog"><div id="collections-action-dialog" class="dialog collections-dialog" aria-hidden="true"><div class="title">Add to Collections</div><div class="collections-action-panel action-panel"><form id="collections-action-dialog-form" class="collections-action-panel-form action-panel-content action-form action-panel-smaller-selectors" data-existing-collections-url="/list-existing-collections/" data-add-to-existing-collection-url="/add-to-existing-collection/" data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/" data-myncbi-max-collection-name-length="100" data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/"><input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"><div class="choice-group" role="radiogroup"><ul class="radio-group-items"><li><input type="radio" id="collections-action-dialog-new" class="collections-new" name="collections" value="new" data-ga-category="collections_button" data-ga-action="click" data-ga-label="collections_radio_new"><label for="collections-action-dialog-new">Create a new collection</label></li><li><input type="radio" id="collections-action-dialog-existing" class="collections-existing" name="collections" value="existing" checked="true" data-ga-category="collections_button" data-ga-action="click" data-ga-label="collections_radio_existing"><label for="collections-action-dialog-existing">Add to an existing collection</label></li></ul></div><div class="controls-wrapper"><div class="action-panel-control-wrap new-collections-controls"><label for="collections-action-dialog-add-to-new" class="action-panel-label required-field-asterisk"> Name your collection: </label><input type="text" name="add-to-new-collection" id="collections-action-dialog-add-to-new" class="collections-action-add-to-new" pattern="[^"&=<>\/]*" title="The following characters are not allowed in the Name field: "&=<>/" maxlength="100" data-ga-category="collections_button" data-ga-action="create_collection" data-ga-label="non_favorties_collection"><div class="collections-new-name-too-long usa-input-error-message selection-validation-message"> Name must be less than 100 characters </div></div><div class="action-panel-control-wrap existing-collections-controls"><label for="collections-action-dialog-add-to-existing" class="action-panel-label"> Choose a collection: </label><select id="collections-action-dialog-add-to-existing" class="action-panel-selector collections-action-add-to-existing" data-ga-category="collections_button" data-ga-action="select_collection" data-ga-label="($('.collections-action-add-to-existing').val() === 'Favorites') ? 'Favorites' : 'non_favorites_collection'"></select><div class="collections-retry-load-on-error usa-input-error-message selection-validation-message"> Unable to load your collection due to an error<br><a href="#">Please try again</a></div></div></div><div class="action-panel-actions"><button class="action-panel-submit" type="submit" data-loading-label="Adding..." data-pinger-ignore data-ga-category="collections_button" data-ga-action="click" data-ga-label="add"> Add </button><button class="action-panel-cancel" aria-label="Close 'Add to Collections' panel" ref="linksrc=close_collections_panel" aria-controls="collections-action-panel" aria-expanded="false" data-ga-category="collections_button" data-ga-action="click" data-ga-label="cancel"> Cancel </button></div></form></div></div></div></div><button class="more-actions-button more-actions-dialog-trigger" title="Open dialog with more actions to take" ref="linksrc=more_actions_btn"></button><div class="display-options" data-format-key="format" data-default-format-value="abstract" data-current-format-value="abstract" role="region"><button class="trigger usa-button" title="Change format" data-ga-category="display_options" data-ga-action="display_options_dialog"><span class="button-label">Display options</span></button><div class="dropdown" hidden><div class="title"> Display options </div><div class="content"><div class="format-container"><span class="option-label"> Format </span><select name="format" data-initial-value="abstract" aria-label="Display format" id="sidebar-actions-display-format"><option value="abstract">Abstract</option><option value="pubmed">PubMed</option><option value="pmid">PMID</option></select></div></div></div></div></div></div> <div class="social-sharing"> <h3 class="title"> Share </h3> <ul class="social-sharing-links usa-unstyled-list"> <li> <a href="http://twitter.com/intent/tweet?text=All%20the%20sites%20we%20cannot%20see%3A%20Sources%20and%20mitigation%20of%20false%20negatives%20in%20RNA%20modification%20studies%20https%3A//pubmed.ncbi.nlm.nih.gov/39433914/" class="share-link share-link-twitter" rel="noreferrer noopener" target="Pubmed-Social-Media-Share-Popup" title="Share article on Twitter" data-ga-category="save_share" data-ga-action="social" data-ga-label="twitter"></a> </li> <li> <a href="http://www.facebook.com/sharer/sharer.php?u=https%3A//pubmed.ncbi.nlm.nih.gov/39433914/" class="share-link share-link-facebook" rel="noreferrer noopener" target="Pubmed-Social-Media-Share-Popup" title="Share article on Facebook" data-ga-category="save_share" data-ga-action="social" data-ga-label="fb"></a> </li> <li> <div class="share-permalink"> <button class="trigger" title="Show article permalink" ref="linksrc=show_permalink_btn"> </button> <div class="dropdown" hidden> <div class="title"> Permalink </div> <div class="content"> <input type="text" class="permalink-text" value="https://pubmed.ncbi.nlm.nih.gov/39433914/" aria-label="Article permalink"/><button class="permalink-copy-button usa-button-primary" title="Copy article permalink" data-ga-category="save_share" data-ga-action="link" data-ga-label="copy_link"><span class="button-title">Copy</span></button> </div> </div> </div> </li> </ul> </div> <nav class="page-navigator" role="navigation" aria-label="Page navigation"> <div class="full-view"> <h3 class="title"> Page navigation </h3> <ul class="items-list"> <li class="heading "> <a href="#heading" aria-label="navigate to Title & authors section" data-ga-category="page_nav" data-ga-action="heading"> Title & authors </a> </li> <li class="linked-correction-forward current"> <a href="#linked-correction-forward" aria-label="navigate to Erratum in section" data-ga-category="page_nav" data-ga-action="linked-correction-forward"> Erratum in </a> </li> <li class="abstract "> <a href="#abstract" aria-label="navigate to Abstract section" data-ga-category="page_nav" data-ga-action="abstract"> Abstract </a> </li> <li class="conflict-of-interest "> <a href="#conflict-of-interest" aria-label="navigate to Conflict of interest statement section" data-ga-category="page_nav" data-ga-action="conflict-of-interest"> Conflict of interest statement </a> </li> <li class="similar "> <a href="#similar" aria-label="navigate to Similar articles section" data-ga-category="page_nav" data-ga-action="similar"> Similar articles </a> </li> <li class="references "> <a href="#references" aria-label="navigate to References section" data-ga-category="page_nav" data-ga-action="references"> References </a> </li> <li class="publication-types "> <a href="#publication-types" aria-label="navigate to Publication types section" data-ga-category="page_nav" data-ga-action="publication-types"> Publication types </a> </li> <li class="related-links "> <a href="#related-links" aria-label="navigate to Related information section" data-ga-category="page_nav" data-ga-action="related-links"> Related information </a> </li> <li class="linkout "> <a href="#linkout" aria-label="navigate to LinkOut - more resources section" data-ga-category="page_nav" data-ga-action="linkout"> LinkOut - more resources </a> </li> </ul> </div> <select class="short-view" autocomplete="off" title="navigate to selected section" aria-label="Navigate to page section"> <option value="heading">Title & authors</option> <option value="linked-correction-forward">Erratum in</option> <option value="abstract">Abstract</option> <option value="conflict-of-interest">Conflict of interest statement</option> <option value="similar">Similar articles</option> <option value="references">References</option> <option value="publication-types">Publication types</option> <option value="related-links">Related information</option> <option value="linkout">LinkOut - more resources</option> </select> </nav> </div> </aside> <main class="article-details" id="article-details">   <header class="heading" id="heading"> <div class="full-view" id="full-view-heading"> <div class="article-citation"> <div class="publication-type" >Review</div> <div class="article-source"> <div class="journal-actions dropdown-block"><button id="full-view-journal-trigger" class="journal-actions-trigger trigger" ref="linksrc=journal_actions_btn" title="Nature reviews. Molecular cell biology" tabindex="0" aria-controls="full-view-journal" aria-expanded="false" aria-label="Toggle dropdown menu for journal Nature reviews. Molecular cell biology" data-pinger-ignore> Nat Rev Mol Cell Biol </button><div id="full-view-journal" class="journal-actions-dropdown dropdown dropdown-container" hidden aria-label="Dropdown menu for journal Nature reviews. Molecular cell biology"><div class="title">Actions</div><div class="content"><ul class="journal-actions-links"><li><a class="search-in-pubmed-link dropdown-block-link" href="/?term=%22Nat+Rev+Mol+Cell+Biol%22%5Bjour%5D&sort=date&sort_order=desc" data-href="/?term=%22Nat+Rev+Mol+Cell+Biol%22%5Bjour%5D&sort=date&sort_order=desc" ref="linksrc=search_in_pubmed_journal_name_link&journal_abbrev=Nat Rev Mol Cell Biol" data-ga-category="search" data-ga-action="journal_link" data-ga-label="Nat Rev Mol Cell Biol"> Search in PubMed </a></li><li><a class="search-in-nlm-catalog-link dropdown-block-link" ref ="linksrc=search_in_nlm_catalog_link" href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Nat+Rev+Mol+Cell+Biol%22%5BTitle+Abbreviation%5D" data-ga-category="search_catalog" data-ga-action="journal_link" data-ga-label="Nat Rev Mol Cell Biol"> Search in NLM Catalog </a></li><li><a class="add-to-search-link dropdown-block-link" ref ="linksrc=add_to_search_link" role="button" data-search-term='"Nat Rev Mol Cell Biol"[jour]' data-ga-category="search" data-ga-action="add_to_search" data-ga-label='"Nat Rev Mol Cell Biol"[jour]' href="#"> Add to Search </a></li></ul></div></div></div><span class="period">. </span><span class="cit">2024 Oct 21.</span> </div> <span class="citation-doi"> doi: 10.1038/s41580-024-00784-2. </span> <span class="ahead-of-print"> Online ahead of print. </span> </div> <h1 class="heading-title"> All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies </h1> <div class="inline-authors"> <div class="authors"> <div class="authors-list"> <span class="authors-list-item "><a class="full-name" href="/?term=Oberdoerffer+S&cauthor_id=39433914" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Shalini Oberdoerffer">Shalini Oberdoerffer</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. shalini.oberdoerffer@nih.gov." href="#full-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Gilbert+WV&cauthor_id=39433914" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Wendy V Gilbert">Wendy V Gilbert</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. wendy.gilbert@yale.edu." href="#full-view-affiliation-2" ref="linksrc=author_aff"> 2 </a></sup></span> </div> </div> </div> <div class="short-article-details"> Affiliations <button class="more-details" id="toggle-authors" data-alt-text="Collapse" aria-controls="expanded-authors" aria-expanded="false" data-pinger-ignore data-fetch-url="/39433914/long-authors/" data-id-prefix=""> <span class="title"> Expand </span> </button> </div> <div class="extended-article-details" id="expanded-authors" aria-hidden="true"> <div class="expanded-authors" id="full-view-expanded-authors"> <div class="affiliations"> <h3 class="title"> Affiliations </h3> <ul class="item-list"> <li data-affiliation-id="full-view-affiliation-1" id="full-view-affiliation-1" ><sup class="key">1</sup> Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. shalini.oberdoerffer@nih.gov.</li> <li data-affiliation-id="full-view-affiliation-2" id="full-view-affiliation-2" ><sup class="key">2</sup> Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. wendy.gilbert@yale.edu.</li> </ul> </div> </div> </div> <ul class="identifiers" id="full-view-identifiers"> <li> <span class="identifier pubmed"> <span class="id-label"> PMID: </span> <strong class="current-id" title="PubMed ID">39433914</strong> </span> </li> <li> <span class="identifier doi"> <span class="id-label"> DOI: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=10.1038/s41580-024-00784-2&id_type=DOI" href="https://doi.org/10.1038/s41580-024-00784-2" data-ga-category="full_text" data-ga-action="DOI" > 10.1038/s41580-024-00784-2 </a> </span> </li> </ul> <div class="in-clipboard-label " hidden> Item in Clipboard </div> </div> <div class="short-view" id="short-view-heading"> <div class="publication-type" >Review</div> <h1 class="heading-title"> All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies </h1> <div class="short-citation"> <span class="authors-list"> <span class="authors-list-item "><span class="full-name">Shalini Oberdoerffer</span><span class="citation-separator"> et al.</span></span> </span> <span class="citation-journal"> Nat Rev Mol Cell Biol<span class="citation-separator">.</span> </span> <span class="date"> <time class="citation-year" datetime="2024">2024</time><span class="citation-separator">.</span> </span> </div> <div class="more-article-details-section with-display-settings"> <button class="more-article-details" id="toggle-article-details" data-alt-text="Hide details" ref="linksrc=toggle_article_details" aria-controls="full-article-details" aria-expanded="false" data-fetch-url="/39433914/long-authors/" data-id-prefix=""> <span class="title">Show details</span> </button> <div class="display-options" data-format-key="format" data-default-format-value="abstract" data-current-format-value="abstract" role="region"> <button class="trigger usa-button" title="Change format" data-ga-category="display_options" data-ga-action="display_options_dialog"> <span class="button-label">Display options</span> </button> <div class="dropdown" hidden> <div class="title"> Display options </div> <div class="content"> <div class="format-container"> <span class="option-label"> Format </span> <select name="format" data-initial-value="abstract" aria-label="Display format" id="mobile-display-format"> <option value="abstract">Abstract</option> <option value="pubmed">PubMed</option> <option value="pmid">PMID</option> </select> </div> </div> </div> </div> </div> <div class="extended-article-details" id="full-article-details" aria-hidden="true"> <div class="article-citation"> <div class="article-source"> <div class="journal-actions dropdown-block"><button id="short-view-journal-trigger" class="journal-actions-trigger trigger" ref="linksrc=journal_actions_btn" title="Nature reviews. Molecular cell biology" tabindex="0" aria-controls="short-view-journal" aria-expanded="false" aria-label="Toggle dropdown menu for journal Nature reviews. Molecular cell biology" data-pinger-ignore> Nat Rev Mol Cell Biol </button><div id="short-view-journal" class="journal-actions-dropdown dropdown dropdown-container" hidden aria-label="Dropdown menu for journal Nature reviews. Molecular cell biology"><div class="title">Actions</div><div class="content"><ul class="journal-actions-links"><li><a class="search-in-pubmed-link dropdown-block-link" href="/?term=%22Nat+Rev+Mol+Cell+Biol%22%5Bjour%5D&sort=date&sort_order=desc" data-href="/?term=%22Nat+Rev+Mol+Cell+Biol%22%5Bjour%5D&sort=date&sort_order=desc" ref="linksrc=search_in_pubmed_journal_name_link&journal_abbrev=Nat Rev Mol Cell Biol" data-ga-category="search" data-ga-action="journal_link" data-ga-label="Nat Rev Mol Cell Biol"> Search in PubMed </a></li><li><a class="search-in-nlm-catalog-link dropdown-block-link" ref ="linksrc=search_in_nlm_catalog_link" href="https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Nat+Rev+Mol+Cell+Biol%22%5BTitle+Abbreviation%5D" data-ga-category="search_catalog" data-ga-action="journal_link" data-ga-label="Nat Rev Mol Cell Biol"> Search in NLM Catalog </a></li><li><a class="add-to-search-link dropdown-block-link" ref ="linksrc=add_to_search_link" role="button" data-search-term='"Nat Rev Mol Cell Biol"[jour]' data-ga-category="search" data-ga-action="add_to_search" data-ga-label='"Nat Rev Mol Cell Biol"[jour]' href="#"> Add to Search </a></li></ul></div></div></div><span class="period">. </span><span class="cit">2024 Oct 21.</span> </div> <span class="citation-doi"> doi: 10.1038/s41580-024-00784-2. </span> <span class="ahead-of-print"> Online ahead of print. </span> </div> <div class="expanded-authors" id="short-view-expanded-authors"> <div class="authors"> <h3 class="title"> Authors </h3> <div class="authors-list"> <span class="authors-list-item "><a class="full-name" href="/?term=Oberdoerffer+S&cauthor_id=39433914" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Shalini Oberdoerffer">Shalini Oberdoerffer</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. shalini.oberdoerffer@nih.gov." href="#short-view-affiliation-1" ref="linksrc=author_aff"> 1 </a></sup><span class="comma">, </span></span><span class="authors-list-item "><a class="full-name" href="/?term=Gilbert+WV&cauthor_id=39433914" ref="linksrc=author_name_link" data-ga-category="search" data-ga-action="author_link" data-ga-label="Wendy V Gilbert">Wendy V Gilbert</a><sup class="affiliation-links"><span class="author-sup-separator"> </span><a class="affiliation-link" title="Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. wendy.gilbert@yale.edu." href="#short-view-affiliation-2" ref="linksrc=author_aff"> 2 </a></sup></span> </div> </div> <div class="affiliations"> <h3 class="title"> Affiliations </h3> <ul class="item-list"> <li data-affiliation-id="short-view-affiliation-1" id="short-view-affiliation-1" ><sup class="key">1</sup> Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. shalini.oberdoerffer@nih.gov.</li> <li data-affiliation-id="short-view-affiliation-2" id="short-view-affiliation-2" ><sup class="key">2</sup> Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. wendy.gilbert@yale.edu.</li> </ul> </div> </div> <ul class="identifiers" id="short-view-identifiers"> <li> <span class="identifier pubmed"> <span class="id-label"> PMID: </span> <strong class="current-id" title="PubMed ID">39433914</strong> </span> </li> <li> <span class="identifier doi"> <span class="id-label"> DOI: </span> <a class="id-link" target="_blank" rel="noopener" ref="linksrc=article_id_link&article_id=10.1038/s41580-024-00784-2&id_type=DOI" href="https://doi.org/10.1038/s41580-024-00784-2" data-ga-category="full_text" data-ga-action="DOI" > 10.1038/s41580-024-00784-2 </a> </span> </li> </ul> <div class="in-clipboard-label " hidden> Item in Clipboard </div> </div> </div> </header> <div class="actions-buttons inline"><div class="inner-wrap"><button class="full-text-links-button full-text-links-dialog-trigger" title="Open dialog with full text links" ref="linksrc=full_text_links"> Full text links </button><button class="citation-button citation-dialog-trigger" aria-label="Open dialog with citation text in different styles" data-ga-category="save_share" data-ga-action="cite" data-ga-label="open" data-all-citations-url="/39433914/citations/" data-citation-style="nlm" data-pubmed-format-link="/39433914/export/"><span class="button-label">Cite</span></button><button class="more-actions-button more-actions-dialog-trigger" title="Open dialog with more actions to take" ref="linksrc=more_actions_btn"></button><div class="display-options" data-format-key="format" data-default-format-value="abstract" data-current-format-value="abstract" role="region"><button class="trigger usa-button" title="Change format" data-ga-category="display_options" data-ga-action="display_options_dialog"><span class="button-label">Display options</span></button><div class="dropdown" hidden><div class="title"> Display options </div><div class="content"><div class="format-container"><span class="option-label"> Format </span><select name="format" data-initial-value="abstract" aria-label="Display format" id="inline-actions-display-format"><option value="abstract">Abstract</option><option value="pubmed">PubMed</option><option value="pmid">PMID</option></select></div></div></div></div></div></div> <div class="linked-articles" id="linked-correction-forward"> <h2 class="title"> Erratum in </h2> <ul class="item-list usa-unstyled-list"> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/39533117/" ref="article_id=39533117&linksrc=comments_link" data-ga-category="comment_correction" data-ga-action="abstract_page_link" data-ga-label="linked-correction-forward"> Author Correction: All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Oberdoerffer S, Gilbert WV.</span> <span class="docsum-authors short-authors">Oberdoerffer S, et al.</span> <span class="docsum-journal-citation full-journal-citation">Nat Rev Mol Cell Biol. 2024 Nov 12. doi: 10.1038/s41580-024-00810-3. Online ahead of print.</span> <span class="docsum-journal-citation short-journal-citation">Nat Rev Mol Cell Biol. 2024.</span> <span class="citation-part">PMID: <span class="docsum-pmid">39533117</span></span> <span class="no-abstract spaced-citation-item citation-part">No abstract available.</span> </div> </div> </li> </ul> </div> <div class="abstract" id="abstract"> <h2 class="title"> Abstract </h2> <div class="abstract-content selected" id="eng-abstract"> <p> RNA modifications are essential for human health - too much or too little of them leads to serious illnesses ranging from neurodevelopmental disorders to cancer. Technical advances in RNA modification sequencing are beginning to uncover the RNA targets of diverse RNA-modifying enzymes that are dysregulated in disease. However, the emerging transcriptome-wide maps of modified nucleosides installed by these enzymes should be considered as first drafts. In particular, a range of technical artefacts lead to false negatives - modified sites that are overlooked owing to technique-dependent, and often sequence-context-specific, 'blind spots'. In this Review, we discuss potential sources of false negatives in sequencing-based RNA modification maps, propose mitigation strategies and suggest guidelines for transparent reporting of sensitivity to detect modified sites in profiling studies. Important considerations for recognition and avoidance of false negatives include assessment and reporting of position-specific sequencing depth, identification of protocol-dependent RNA capture biases and applying controls for false negatives as well as for false positives. Despite their limitations, emerging maps of RNA modifications reveal exciting and largely uncharted potential for post-transcriptional control of all aspects of RNA function. </p> </div> </div> <p class="copyright" id="copyright"> © 2024. Springer Nature Limited. </p> <p class="disclaimer" id="disclaimer"> <a href="/disclaimer/" target="_blank" ga_category="literature_resources" ga_action="disclaimer_link" ga_label="under_abstract">PubMed Disclaimer</a> </p> <div class="conflict-of-interest" id="conflict-of-interest"> <h2 class="title"> Conflict of interest statement </h2> <div class="statement"> <p xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:p1="http://pubmed.gov/pub-one"><bold>Competing interests</bold> The authors declare no competing interests.</p> </div> </div> <div class="similar-articles" id="similar"> <h2 class="title"> Similar articles </h2> <ul class="articles-list" id="similar-articles-list"> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/37733063/" ref="article_id=37733063&linksrc=similar_articles_link&ordinalpos=1" data-ga-category="similar_article" data-ga-action="37733063" data-ga-label=""> Chemoproteomic Approaches to Studying RNA Modification-Associated Proteins. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Dai W, Yu NJ, Kleiner RE.</span> <span class="docsum-authors short-authors">Dai W, et al.</span> <span class="docsum-journal-citation full-journal-citation">Acc Chem Res. 2023 Oct 3;56(19):2726-2739. doi: 10.1021/acs.accounts.3c00450. Epub 2023 Sep 21.</span> <span class="docsum-journal-citation short-journal-citation">Acc Chem Res. 2023.</span> <span class="citation-part">PMID: <span class="docsum-pmid">37733063</span></span> <span class="free-resources spaced-citation-item citation-part">Free PMC article.</span> </div> </div> </li> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/38966972/" ref="article_id=38966972&linksrc=similar_articles_link&ordinalpos=2" data-ga-category="similar_article" data-ga-action="38966972" data-ga-label=""> [Advances in mapping analysis of ribonucleic acid modifications through sequencing]. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Xiong J, Feng T, Yuan BF.</span> <span class="docsum-authors short-authors">Xiong J, et al.</span> <span class="docsum-journal-citation full-journal-citation">Se Pu. 2024 Jul;42(7):632-645. doi: 10.3724/SP.J.1123.2023.12025.</span> <span class="docsum-journal-citation short-journal-citation">Se Pu. 2024.</span> <span class="citation-part">PMID: <span class="docsum-pmid">38966972</span></span> <span class="free-resources spaced-citation-item citation-part">Free PMC article.</span> <span class="publication-type spaced-citation-item citation-part">Review.</span> <span class="language spaced-citation-item citation-part">Chinese.</span> </div> </div> </li> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/39533117/" ref="article_id=39533117&linksrc=similar_articles_link&ordinalpos=3" data-ga-category="similar_article" data-ga-action="39533117" data-ga-label=""> Author Correction: All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Oberdoerffer S, Gilbert WV.</span> <span class="docsum-authors short-authors">Oberdoerffer S, et al.</span> <span class="docsum-journal-citation full-journal-citation">Nat Rev Mol Cell Biol. 2024 Nov 12. doi: 10.1038/s41580-024-00810-3. Online ahead of print.</span> <span class="docsum-journal-citation short-journal-citation">Nat Rev Mol Cell Biol. 2024.</span> <span class="citation-part">PMID: <span class="docsum-pmid">39533117</span></span> <span class="no-abstract spaced-citation-item citation-part">No abstract available.</span> </div> </div> </li> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/36321557/" ref="article_id=36321557&linksrc=similar_articles_link&ordinalpos=4" data-ga-category="similar_article" data-ga-action="36321557" data-ga-label=""> Folic acid supplementation and malaria susceptibility and severity among people taking antifolate antimalarial drugs in endemic areas. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Crider K, Williams J, Qi YP, Gutman J, Yeung L, Mai C, Finkelstain J, Mehta S, Pons-Duran C, Menéndez C, Moraleda C, Rogers L, Daniels K, Green P.</span> <span class="docsum-authors short-authors">Crider K, et al.</span> <span class="docsum-journal-citation full-journal-citation">Cochrane Database Syst Rev. 2022 Feb 1;2(2022):CD014217. doi: 10.1002/14651858.CD014217.</span> <span class="docsum-journal-citation short-journal-citation">Cochrane Database Syst Rev. 2022.</span> <span class="citation-part">PMID: <span class="docsum-pmid">36321557</span></span> <span class="free-resources spaced-citation-item citation-part">Free PMC article.</span> </div> </div> </li> <li class="full-docsum"> <div class="docsum-content" style="display:inline;"> <a class="docsum-title" href="/38460080/" ref="article_id=38460080&linksrc=similar_articles_link&ordinalpos=5" data-ga-category="similar_article" data-ga-action="38460080" data-ga-label=""> When to Pull the Trigger: Conceptual Considerations for Approximating Head Acceleration Events Using Instrumented Mouthguards. </a> <div class="docsum-citation full-citation"> <span class="docsum-authors full-authors">Tooby J, Till K, Gardner A, Stokes K, Tierney G, Weaving D, Rowson S, Ghajari M, Emery C, Bussey MD, Jones B.</span> <span class="docsum-authors short-authors">Tooby J, et al.</span> <span class="docsum-journal-citation full-journal-citation">Sports Med. 2024 Jun;54(6):1361-1369. doi: 10.1007/s40279-024-02012-5. Epub 2024 Mar 9.</span> <span class="docsum-journal-citation short-journal-citation">Sports Med. 2024.</span> <span class="citation-part">PMID: <span class="docsum-pmid">38460080</span></span> <span class="free-resources spaced-citation-item citation-part">Free PMC article.</span> <span class="publication-type spaced-citation-item citation-part">Review.</span> </div> </div> </li> </ul> <div class="actions-bar"> <a class="show-all-linked-articles" data-href="/?linkname=pubmed_pubmed&from_uid=39433914" data-ga-category="similar_article" data-ga-action="show_all" > See all similar articles </a> </div> </div> <div class="references" id="references"> <h2 class="title"> References </h2> <div id='top-references-list' class="references-lists-container"> <div class="refs-list"> <ol id="top-references-list-1" class="references-list"> <li> <ol class="references-and-notes-list"> <li class="skip-numbering" value="1"> Cappannini, A. et al. MODOMICS: a database of RNA modifications and related information. 2023 update. Nucleic Acids Res. 52, D239–D244 (2024). - <a class="reference-link" href="/38015436/" ref="linksrc=references_link&ordinalpos=1" data-ga-category="reference" data-ga-action="38015436" > PubMed </a> - <a class="reference-link" href="https://doi.org/10.1093/nar/gkad1083" ref="linksrc=references_link&ordinalpos=2" data-ga-category="reference" data-ga-action="10.1093/nar/gkad1083" > DOI </a> </li> </ol> </li> <li> <ol class="references-and-notes-list"> <li class="skip-numbering" value="1"> Gilbert, W. V. & Nachtergaele, S. mRNA regulation by RNA modifications. Annu. Rev. Biochem. 92, 175–198 (2023). - <a class="reference-link" href="/37018844/" ref="linksrc=references_link&ordinalpos=1" data-ga-category="reference" data-ga-action="37018844" > PubMed </a> - <a class="reference-link" href="https://pmc.ncbi.nlm.nih.gov/articles/11192554/" ref="linksrc=references_link&ordinalpos=2" data-ga-category="reference" data-ga-action="11192554" > PMC </a> - <a class="reference-link" href="https://doi.org/10.1146/annurev-biochem-052521-035949" ref="linksrc=references_link&ordinalpos=3" data-ga-category="reference" data-ga-action="10.1146/annurev-biochem-052521-035949" > DOI </a> </li> </ol> </li> <li> <ol class="references-and-notes-list"> <li class="skip-numbering" value="1"> Qiu, L., Jing, Q., Li, Y. B. & Han, J. H. RNA modification: mechanisms and therapeutic targets. Mol. Biomed. 4, 56 (2023). - <a class="reference-link" href="https://doi.org/10.1186/s43556-023-00139-x" ref="linksrc=references_link&ordinalpos=1" data-ga-category="reference" data-ga-action="10.1186/s43556-023-00139-x" > DOI </a> </li> </ol> </li> <li> <ol class="references-and-notes-list"> <li class="skip-numbering" value="1"> Islam, S. et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat. Methods 11, 163–166 (2014). - <a class="reference-link" href="/24363023/" ref="linksrc=references_link&ordinalpos=1" data-ga-category="reference" data-ga-action="24363023" > PubMed </a> - <a class="reference-link" href="https://doi.org/10.1038/nmeth.2772" ref="linksrc=references_link&ordinalpos=2" data-ga-category="reference" data-ga-action="10.1038/nmeth.2772" > DOI </a> </li> </ol> </li> <li> <ol class="references-and-notes-list"> <li class="skip-numbering" value="1"> Zenklusen, D., Larson, D. R. & Singer, R. H. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat. Struct. Mol. Biol. 15, 1263–1271 (2008). - <a class="reference-link" href="/19011635/" ref="linksrc=references_link&ordinalpos=1" data-ga-category="reference" data-ga-action="19011635" > PubMed </a> - <a class="reference-link" href="https://pmc.ncbi.nlm.nih.gov/articles/3154325/" ref="linksrc=references_link&ordinalpos=2" data-ga-category="reference" data-ga-action="3154325" > PMC </a> - <a class="reference-link" href="https://doi.org/10.1038/nsmb.1514" ref="linksrc=references_link&ordinalpos=3" data-ga-category="reference" data-ga-action="10.1038/nsmb.1514" > DOI </a> </li> </ol> </li> </ol> <div class="actions-bar"> <button class="show-all" ref="linksrc=show_all_references_link" aria-controls="top-references-list-1" data-next-page-url="/39433914/references/" data-ga-category="reference" data-ga-action="show_more" > Show all 78 references </button> </div> </div> </div> </div> <div id="publication-types" class="publication-types keywords-section"> <h2 class="title"> Publication types </h2> <ul class="keywords-list"><li><div class="keyword-actions dropdown-block"><button class="keyword-actions-trigger trigger keyword-link" aria-label="Toggle dropdown menu for keyword Review" tabindex="0" aria-controls="keyword-actions-publication-types-0" aria-expanded="false" data-pinger-ignore> Review </button><div id="keyword-actions-publication-types-0" class="keyword-actions-dropdown dropdown dropdown-container" hidden aria-label="Dropdown menu for keyword Review"><div class="title">Actions</div><div class="content"><ul class="keyword-actions-links"><li><a class="search-in-pubmed-link dropdown-block-link" href="/?term=%22Review%22%5Bpt%5D&sort=date&sort_order=desc" data-href="/?term=%22Review%22%5Bpt%5D&sort=date&sort_order=desc" ref="linksrc=search_in_pubmed_keyword_link&keyword="Review"[pt]" data-ga-category="search" data-ga-action="pub_type" data-ga-label="Review"> Search in PubMed </a></li><li><a class="search-in-mesh-link dropdown-block-link" ref="linksrc=search_in_mesh_link" href="https://www.ncbi.nlm.nih.gov/mesh?term=Review" data-ga-category="search_mesh" data-ga-action="pub_type_link" data-ga-label="Review"> Search in MeSH </a></li><li><a class="add-to-search-link dropdown-block-link" ref="linksrc=add_to_search_link" role="button" data-search-term=""Review"[pt]" data-ga-category="search" data-ga-action="add_to_search" data-ga-label=""Review"[pt]" href="#"> Add to Search </a></li></ul></div></div></div></li></ul> </div> <div id="related-links" class="related-links"> <h2 class="title"> Related information </h2> <ul class="related-links-list"><li><a title="Related information in MedGen" href="https://www.ncbi.nlm.nih.gov/medgen?linkname=pubmed_medgen&from_uid=39433914" ref="log$=recordlinks&logdbfrom=pubmed&ncbi_uid=39433914&ordinalpos=1&linkpos=1"> MedGen </a></li></ul> </div> <div id="linkout" class="linkout"> <h2 class="title"> LinkOut - more resources </h2> <ul class="linkout-list"><li><h3 class="linkout-category">Full Text Sources</h3><ul class="linkout-category-links"><li><a href="https://doi.org/10.1038/s41580-024-00784-2" target="_blank" rel="noopener" ref="linksrc=linkout_link&PrId=3094&uid=39433914&db=pubmed&itool=Abstract&log$=linkoutlink&nlmid=100962782" data-ga-category="link_out" data-ga-action="Full Text Sources" data-ga-label="Nature Publishing Group" > Nature Publishing Group </a></li></ul></li></ul> </div> </main> <div class="overlay" role="dialog" aria-label="Full Text Links Dialog"> <div id="full-text-links-dialog" class="dialog full-text-links-dialog"> <strong class="title">Full text links</strong> <button class="close-overlay" tabindex="2">[x]</button> <div class="full-text-links-list"> <a class="link-item dialog-focus" href="https://doi.org/10.1038/s41580-024-00784-2" target="_blank" rel="noopener" ref="linksrc=fulltextorjournal_fulltext&is_pmc=False&PrId=3094&itool=Abstract-def&log$=linkouticon&uid=39433914&db=pubmed&nlmid=100962782" title="See full text options at Nature Publishing Group" tabindex="1" data-ga-category="full_text" data-ga-action="Nature Publishing Group" data-ga-label="39433914" ><img src="https://cdn.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--www.nature.com-static-images-logos-nature-portfolio-120.png" alt="full text provider logo"><span class="text"> Nature Publishing Group </span></a> </div> </div> </div> <div class="overlay" role="dialog" aria-label="Citation Dialog"> <div class="dialog citation-dialog"> <button class="close-overlay" tabindex="1">[x]</button> <div class="title">Cite</div> <div class="citation-text-block"> <div class="citation-text"></div> <div class="citation-actions"> <button class="copy-button dialog-focus" data-ga-category="save_share" data-ga-action="cite" data-ga-label="copy" tabindex="2"> Copy </button> <form method="post"> <input type="hidden" name="csrfmiddlewaretoken" value="kXUhE0Lr8KU0q7yiA7PrHyJsfWg0BN5SvQNZGvsP5cPQK22X7IZCEA1lMN2Xx7zt"> <button type="submit" class="export-button" data-ga-category="save_share" data-ga-action="cite" data-ga-label="download" title="Download a file for external citation management software" tabindex="3"> <span class="download-title">Download .nbib</span> <span class="download-title-mobile">.nbib</span> </button> </form> <div class="citation-style-selector-wrapper"> <label class="selector-label">Format:</label> <select aria-label="Format" class="citation-style-selector" tabindex="4"> <option data-style-url-name="ama" value="AMA" > AMA </option> <option data-style-url-name="apa" value="APA" > APA </option> <option data-style-url-name="mla" value="MLA" > MLA </option> <option data-style-url-name="nlm" value="NLM" selected="selected"> NLM </option> </select> </div> </div> </div> </div> </div> <div class="overlay" role="dialog" aria-label="More Actions Dialog"> <div id="more-actions-dialog" class="dialog more-actions-dialog"> <strong class="title">Send To</strong> <ul class="more-actions-links"> <li><a id="clipboard-trigger" role="button" class="submit-button clipboard-trigger clipboard-trigger-target dialog-focus link-item " href="#">Clipboard</a></li> <li><a class="email-trigger link-item" role="button" href="#">Email</a></li> <li><a class="save-trigger link-item" role="button" href="#">Save</a></li> <li><a class="link-item" role="button" href="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39433914%2F%23open-bibliography-panel">My Bibliography</a></li> <li><a class="link-item" role="button" href="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39433914%2F%23open-collections-panel">Collections</a></li> <li><a class="citation-manager-trigger link-item" role="button" href="#">Citation Manager</a></li> </ul> <button class="close-overlay">[x]</button> </div> </div> </div> <div id="ncbi-footer"> <div class="literature-footer" role="complementary" title="Links to NCBI Literature Resources"> <div class="usa-grid"> <p class="literature-footer-text">NCBI Literature Resources</p> <p class="literature-footer-text"> <a class="literature-footer-link" data-ga-category="literature_resources" data-ga-action="mesh_link" href="https://www.ncbi.nlm.nih.gov/mesh/">MeSH</a> <a class="literature-footer-link" data-ga-category="literature_resources" data-ga-action="pmc_link" href="https://www.ncbi.nlm.nih.gov/pmc/">PMC</a> <a class="literature-footer-link" data-ga-category="literature_resources" data-ga-action="bookshelf_link" href="https://www.ncbi.nlm.nih.gov/books">Bookshelf</a> <a class="literature-footer-link" data-ga-category="literature_resources" data-ga-action="disclaimer_link" href="/disclaimer/">Disclaimer</a> </p> <p class="literature-footer-text attribution-statement">The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.</p> </div> </div>  <footer> <section class="icon-section"> <div id="icon-section-header" class="icon-section_header">Follow NCBI</div> <div class="grid-container container"> <div class="icon-section_container"> <a class="footer-icon" id="footer_twitter" href="https://twitter.com/ncbi" aria-label="Twitter"> <svg width="40" height="40" viewBox="0 0 40 37" fill="none" xmlns="http://www.w3.org/2000/svg"> <title>Twitter</title> <g id="twitterx1008"> <path id="path1008" d="M6.06736 7L16.8778 20.8991L6.00001 32.2H10.2L18.6 23.1L25.668 32.2H34L22.8 17.5L31.9 7H28.4L20.7 15.4L14.401 7H6.06898H6.06736ZM9.66753 8.73423H12.9327L29.7327 30.4658H26.5697L9.66753 8.73423Z" fill="#5B616B"/> </g> </svg> </a> <a class="footer-icon" id="footer_facebook" href="https://www.facebook.com/ncbi.nlm" aria-label="Facebook"><svg data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 300"> <title>Facebook</title> <path class="cls-11" d="M210.5,115.12H171.74V97.82c0-8.14,5.39-10,9.19-10h27.14V52l-39.32-.12c-35.66,0-42.42,26.68-42.42,43.77v19.48H99.09v36.32h27.24v109h45.41v-109h35Z"> </path> </svg></a> <a class="footer-icon" id="footer_linkedin" href="https://www.linkedin.com/company/ncbinlm" aria-label="LinkedIn"><svg data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 300"> <title>LinkedIn</title> <path class="cls-11" d="M101.64,243.37H57.79v-114h43.85Zm-22-131.54h-.26c-13.25,0-21.82-10.36-21.82-21.76,0-11.65,8.84-21.15,22.33-21.15S101.7,78.72,102,90.38C102,101.77,93.4,111.83,79.63,111.83Zm100.93,52.61A17.54,17.54,0,0,0,163,182v61.39H119.18s.51-105.23,0-114H163v13a54.33,54.33,0,0,1,34.54-12.66c26,0,44.39,18.8,44.39,55.29v58.35H198.1V182A17.54,17.54,0,0,0,180.56,164.44Z"> </path> </svg></a> <a class="footer-icon" id="footer_github" href="https://github.com/ncbi" aria-label="GitHub"><svg data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 300"> <defs> <style> .cls-11, .cls-12 { fill: #737373; } .cls-11 { fill-rule: evenodd; } </style> </defs> <title>GitHub</title> <path class="cls-11" d="M151.36,47.28a105.76,105.76,0,0,0-33.43,206.1c5.28,1,7.22-2.3,7.22-5.09,0-2.52-.09-10.85-.14-19.69-29.42,6.4-35.63-12.48-35.63-12.48-4.81-12.22-11.74-15.47-11.74-15.47-9.59-6.56.73-6.43.73-6.43,10.61.75,16.21,10.9,16.21,10.9,9.43,16.17,24.73,11.49,30.77,8.79,1-6.83,3.69-11.5,6.71-14.14C108.57,197.1,83.88,188,83.88,147.51a40.92,40.92,0,0,1,10.9-28.39c-1.1-2.66-4.72-13.42,1-28,0,0,8.88-2.84,29.09,10.84a100.26,100.26,0,0,1,53,0C198,88.3,206.9,91.14,206.9,91.14c5.76,14.56,2.14,25.32,1,28a40.87,40.87,0,0,1,10.89,28.39c0,40.62-24.74,49.56-48.29,52.18,3.79,3.28,7.17,9.71,7.17,19.58,0,14.15-.12,25.54-.12,29,0,2.82,1.9,6.11,7.26,5.07A105.76,105.76,0,0,0,151.36,47.28Z"> </path> <path class="cls-12" d="M85.66,199.12c-.23.52-1.06.68-1.81.32s-1.2-1.06-.95-1.59,1.06-.69,1.82-.33,1.21,1.07.94,1.6Zm-1.3-1"> </path> <path class="cls-12" d="M90,203.89c-.51.47-1.49.25-2.16-.49a1.61,1.61,0,0,1-.31-2.19c.52-.47,1.47-.25,2.17.49s.82,1.72.3,2.19Zm-1-1.08"> </path> <path class="cls-12" d="M94.12,210c-.65.46-1.71,0-2.37-.91s-.64-2.07,0-2.52,1.7,0,2.36.89.65,2.08,0,2.54Zm0,0"></path> <path class="cls-12" d="M99.83,215.87c-.58.64-1.82.47-2.72-.41s-1.18-2.06-.6-2.7,1.83-.46,2.74.41,1.2,2.07.58,2.7Zm0,0"> </path> <path class="cls-12" d="M107.71,219.29c-.26.82-1.45,1.2-2.64.85s-2-1.34-1.74-2.17,1.44-1.23,2.65-.85,2,1.32,1.73,2.17Zm0,0"> </path> <path class="cls-12" d="M116.36,219.92c0,.87-1,1.59-2.24,1.61s-2.29-.68-2.3-1.54,1-1.59,2.26-1.61,2.28.67,2.28,1.54Zm0,0"> </path> <path class="cls-12" d="M124.42,218.55c.15.85-.73,1.72-2,1.95s-2.37-.3-2.52-1.14.73-1.75,2-2,2.37.29,2.53,1.16Zm0,0"></path> </svg></a> <a class="footer-icon" id="footer_blog" href="https://ncbiinsights.ncbi.nlm.nih.gov/" aria-label="Blog"> <svg id="Layer_1" data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 40 40"><defs><style>.cls-1{fill:#737373;}</style></defs><path class="cls-1" d="M14,30a4,4,0,1,1-4-4,4,4,0,0,1,4,4Zm11,3A19,19,0,0,0,7.05,15a1,1,0,0,0-1,1v3a1,1,0,0,0,.93,1A14,14,0,0,1,20,33.07,1,1,0,0,0,21,34h3a1,1,0,0,0,1-1Zm9,0A28,28,0,0,0,7,6,1,1,0,0,0,6,7v3a1,1,0,0,0,1,1A23,23,0,0,1,29,33a1,1,0,0,0,1,1h3A1,1,0,0,0,34,33Z"/></svg> </a> </div> </div> </section> <section class="container-fluid bg-primary"> <div class="container pt-5"> <div class="row mt-3"> <div class="col-lg-3 col-12"> <p><a class="text-white" href="https://www.nlm.nih.gov/socialmedia/index.html">Connect with NLM</a></p> <ul class="list-inline social_media"> <li class="list-inline-item"><a href="https://twitter.com/NLM_NIH" aria-label="Twitter" target="_blank" rel="noopener noreferrer"> <svg width="35" height="35" viewBox="0 0 38 35" fill="none" xmlns="http://www.w3.org/2000/svg"> <title>Twitter</title> <g id="twitterx1009" clip-path="url(#clip0_65276_3946)"> <path id="Vector" d="M17.5006 34.6565C26.9761 34.6565 34.6575 26.9751 34.6575 17.4996C34.6575 8.02416 26.9761 0.342773 17.5006 0.342773C8.02514 0.342773 0.34375 8.02416 0.34375 17.4996C0.34375 26.9751 8.02514 34.6565 17.5006 34.6565Z" fill="#205493" stroke="white" stroke-width="1.2" stroke-miterlimit="10"></path> <path id="path1009" d="M8.54811 8.5L16.2698 18.4279L8.50001 26.5H11.5L17.5 20L22.5486 26.5H28.5L20.5 16L27 8.5H24.5L19 14.5L14.5007 8.5H8.54927H8.54811ZM11.1197 9.73873H13.4519L25.4519 25.2613H23.1926L11.1197 9.73873Z" fill="white"></path> </g> <defs> <clipPath id="clip0_65276_3946"> <rect width="38" height="38" fill="white"></rect> </clipPath> </defs> </svg></a> </li> <li class="list-inline-item"><a href="https://www.facebook.com/nationallibraryofmedicine" aria-label="Facebook" rel="noopener noreferrer" target="_blank"> <svg version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve"> <style type="text/css"> .st10 { fill: #FFFFFF; } .st110 { fill: none; stroke: #FFFFFF; stroke-width: 8; stroke-miterlimit: 10; } </style> <title>SM-Facebook</title> <g> <g> <path class="st10" d="M159,99.1h-24V88.4c0-5,3.3-6.2,5.7-6.2h16.8V60l-24.4-0.1c-22.1,0-26.2,16.5-26.2,27.1v12.1H90v22.5h16.9 v67.5H135v-67.5h21.7L159,99.1z"></path> </g> </g> <circle class="st110" cx="123.6" cy="123.2" r="108.2"></circle> </svg> </a></li> <li class="list-inline-item"><a href="https://www.youtube.com/user/NLMNIH" aria-label="Youtube" target="_blank" rel="noopener noreferrer"><svg version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 249 249" style="enable-background:new 0 0 249 249;" xml:space="preserve"> <title>SM-Youtube</title> <style type="text/css"> .st4 { fill: none; stroke: #FFFFFF; stroke-width: 8; stroke-miterlimit: 10; } .st5 { fill: #FFFFFF; } </style> <circle class="st4" cx="124.2" cy="123.4" r="108.2"></circle> <g transform="translate(0,-952.36218)"> <path class="st5" d="M88.4,1037.4c-10.4,0-18.7,8.3-18.7,18.7v40.1c0,10.4,8.3,18.7,18.7,18.7h72.1c10.4,0,18.7-8.3,18.7-18.7 v-40.1c0-10.4-8.3-18.7-18.7-18.7H88.4z M115.2,1058.8l29.4,17.4l-29.4,17.4V1058.8z"></path> </g> </svg></a></li> </ul> </div> <div class="col-lg-3 col-12"> <p class="address_footer text-white">National Library of Medicine<br> <a href="https://www.google.com/maps/place/8600+Rockville+Pike,+Bethesda,+MD+20894/@38.9959508,-77.101021,17z/data=!3m1!4b1!4m5!3m4!1s0x89b7c95e25765ddb:0x19156f88b27635b8!8m2!3d38.9959508!4d-77.0988323" class="text-white" target="_blank" rel="noopener noreferrer">8600 Rockville Pike<br> Bethesda, MD 20894</a></p> </div> <div class="col-lg-3 col-12 centered-lg"> <p><a href="https://www.nlm.nih.gov/web_policies.html" class="text-white">Web Policies</a><br> <a href="https://www.nih.gov/institutes-nih/nih-office-director/office-communications-public-liaison/freedom-information-act-office" class="text-white">FOIA</a><br> <a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html" class="text-white" id="vdp">HHS Vulnerability Disclosure</a></p> </div> <div class="col-lg-3 col-12 centered-lg"> <p><a class="supportLink text-white" href="https://support.nlm.nih.gov/">Help</a><br> <a href="https://www.nlm.nih.gov/accessibility.html" class="text-white">Accessibility</a><br> <a href="https://www.nlm.nih.gov/careers/careers.html" class="text-white">Careers</a></p> </div> </div> <div class="row"> <div class="col-lg-12 centered-lg"> <nav class="bottom-links"> <ul class="mt-3"> <li> <a class="text-white" href="//www.nlm.nih.gov/">NLM</a> </li> <li> <a class="text-white" href="https://www.nih.gov/">NIH</a> </li> <li> <a class="text-white" href="https://www.hhs.gov/">HHS</a> </li> <li> <a class="text-white" href="https://www.usa.gov/">USA.gov</a> </li> </ul> </nav> </div> </div> </div> </section> </footer>   <script type="text/javascript"> var nwds_version = "1.2.3"; var meta_nwds_ver = document.createElement('meta'); meta_nwds_ver.name = 'ncbi_nwds_ver'; meta_nwds_ver.content = nwds_version; document.getElementsByTagName('head')[0].appendChild(meta_nwds_ver); var meta_nwds = document.createElement('meta'); meta_nwds.name = 'ncbi_nwds'; meta_nwds.content = 'yes'; document.getElementsByTagName('head')[0].appendChild(meta_nwds); var alertsUrl = "/core/alerts/alerts.js"; if (typeof ncbiBaseUrl !== 'undefined') { alertsUrl = ncbiBaseUrl + alertsUrl; } </script> </div>  <script src="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/CACHE/js/output.293fbf76aa18.js"></script>  <script src="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/CACHE/js/output.550e9c8906a2.js"></script> <script> ncbi.awesome.basePage.init({ userInfo: { isLoggedIn: false, username: "", loginUrl: "https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F39433914%2F", logoutUrl: "https://www.ncbi.nlm.nih.gov/account/signout/?back_url=https%3A//pubmed.ncbi.nlm.nih.gov/39433914/" }, baseUrl: 'https://www.ncbi.nlm.nih.gov', noSessionCookieName: "pm-ns", searchIdCookieName: "pm-sid", adjNavSearchIdCookieName: "pm-adjnav-sid", searchFormSubmittedCookieName: "pm-sfs", isOnSearchPageCookieName: "pm-iosp", backToSearchCookieName: "pm-btsl", clinicalSeeAllCookieName: "pm-csa", jsCookieDomain: "pubmed.ncbi.nlm.nih.gov", userShareRequestFailed: "", noSharedSettings: "myncbi_no_shared_settings", noSharedAccount: "myncbi_no_shared_account" }); </script> <script type="module"> import dismissableNCBIAlert from "https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/core/dismissable-ncbi-alert.js"; jQuery.getScript("https://www.ncbi.nlm.nih.gov/core/alerts/alerts.js", function () { galert(['body > *:last-child']); dismissableNCBIAlert(); }).fail(function() { }); </script> <script defer type="text/javascript" src="https://cdn.ncbi.nlm.nih.gov/core/pinger/pinger.js"> </script> <script src="https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/CACHE/js/output.04d45d85d031.js"></script> <script> ncbi.awesome.articlePage.init({ baseSuggestionsUrl: "/suggestions/", mathJaxUrl: "https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/mathjax/unpacked/MathJax.js?config=MML_CHTML", clipboardAPIRoot: "/ajax/clipboard/", clipboardNextPageUrl: "/clipboard-next-page/", searchIdCookieName: "pm-sid", searchFormSubmittedCookieName: "pm-sfs", backToSearchCookieName: "pm-btsl", jsCookieDomain: "pubmed.ncbi.nlm.nih.gov", longTermPrefix: "longquery", adjNavURLPath: "/39433914/adj-nav/", adjNavSearchIdCookieName: "pm-adjnav-sid", articlePageUrl: "/39433914/", markJSUrl: "https://cdn.ncbi.nlm.nih.gov/pubmed/0d576970-ea4f-4f8d-9bab-bf51569c42d2/mark.js/dist/jquery.mark.js", termHighlightColor: "", highlightedTokens: "", citeFormatPreferenceCookieName: "pm-cf" }); </script> </body> </html>

CINXE.COM

All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies - PubMed