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<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="2y8fh7pcrID0LE1bgd9Am51RQA8cY9f9jlSkUXSy1jquF571TwMCQdxvoEQoRKNt">
<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="[^&quot;&amp;=&lt;&gt;\/]*" title="The following characters are not allowed in the Name field: &quot;&amp;=&lt;&gt;/"
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="2y8fh7pcrID0LE1bgd9Am51RQA8cY9f9jlSkUXSy1jquF571TwMCQdxvoEQoRKNt">
<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="2y8fh7pcrID0LE1bgd9Am51RQA8cY9f9jlSkUXSy1jquF571TwMCQdxvoEQoRKNt">
<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="[^&quot;&amp;=&lt;&gt;\/]*" title="The following characters are not allowed in the Name field: &quot;&amp;=&lt;&gt;/">
</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="2y8fh7pcrID0LE1bgd9Am51RQA8cY9f9jlSkUXSy1jquF571TwMCQdxvoEQoRKNt">
<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="2y8fh7pcrID0LE1bgd9Am51RQA8cY9f9jlSkUXSy1jquF571TwMCQdxvoEQoRKNt">
<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="[^&quot;&amp;=&lt;&gt;\/]*" title="The following characters are not allowed in the Name field: &quot;&amp;=&lt;&gt;/">
</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="23973221">
<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://linkinghub.elsevier.com/retrieve/pii/S1074-7613(13)00339-7"
target="_blank"
rel="noopener"
ref="linksrc=fulltextorjournal_fulltext&amp;is_pmc=False&amp;PrId=3048&amp;itool=Abstract-def&amp;log$=linkouticon&amp;uid=23973221&amp;db=pubmed&amp;nlmid=9432918"
title="See full text options at Elsevier Science"
data-ga-category="full_text"
data-ga-action="Elsevier Science"
data-ga-label="23973221"
><img src="https://cdn.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--linkinghub.elsevier.com-ihub-images-celloa.png" alt="Elsevier Science full text link"><span class="text">
Elsevier Science
</span></a><a class="link-item
pmc
"
href="https://pmc.ncbi.nlm.nih.gov/articles/pmid/23973221/"
target="_blank"
rel="noopener"
ref="linksrc=fulltextorjournal_fulltext&amp;is_pmc=True&amp;PrId=3494&amp;itool=Abstract-def&amp;log$=linkouticon&amp;uid=23973221&amp;db=pubmed&amp;nlmid=9432918"
title="Free full text at PubMed Central"
data-ga-category="full_text"
data-ga-action="PMC"
data-ga-label="23973221"
><span class="text">
Free PMC article
</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="/23973221/citations/"
data-citation-style="nlm"
data-pubmed-format-link="/23973221/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="23973221" 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%2F23973221%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="2y8fh7pcrID0LE1bgd9Am51RQA8cY9f9jlSkUXSy1jquF571TwMCQdxvoEQoRKNt"><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"
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<p>
The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH-rearranged gene segment in the 3' proximal Igh domain. By using high-resolution mapping of long-range interactions, we demonstrate that local interaction domains established the three-dimensional structure of the extended Igh locus in lymphoid progenitors. In pro-B cells, these local domains engaged in long-range interactions across the Igh locus, which depend on the regulators Pax5, YY1, and CTCF. The large VH gene cluster underwent flexible long-range interactions with the more rigidly structured proximal domain, which probably ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. These long-range interactions appear to be an intrinsic feature of the VH gene cluster, because they are still generated upon mutation of the Eμ enhancer, IGCR1 insulator, or 3' regulatory region in the proximal Igh domain.
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id="article-image-0"
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<p> Figure 1. High-Resolution Analysis of Long-Range Interactions… </p>
</strong>
</div>
</div>
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Figure 1. High-Resolution Analysis of Long-Range Interactions within the <i> Igh </i> Locus </p>
</strong>
<div class="figure-caption-contents"><p> (A) Interaction of the… </p></div>
</div>
<figcaption id="figure-caption-0" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Figure 1. High-Resolution Analysis of Long-Range Interactions within the <i>Igh</i> Locus
</strong>
<div class="figure-caption-contents">(A) Interaction of the HS3B-HD viewpoint (red) with chromosome 12 sequences in cultured <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> and <i>Rag2<sup>/</sup></i> pro-B cells. The 20 kb running mean values of the 4C-seq reads were plotted as reads per million mapped sequence reads (RPMs). A black bar denotes the <i>Igh</i> locus. (B) Relative distribution of the 4C-seq reads (HS3B-HD viewpoint) in the <i>Igh</i> locus, rest of chromosome 12 (Chr.12 <i>Igh</i>), or entire genome minus chromosome 12 (Genome Chr.12). (C) Pax5-dependent long-range interactions of the HS3B region in ex vivo sorted and in vitro cultured cells of the indicated genotypes. (D) 4C-seq patterns of the HS8-BN and HS8-ED viewpoints in cultured <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> and <i>Rag2<sup>/</sup></i> pro-B cells. A 20 kb running mean mappability track (gray) indicates to what degree (on a scale from 0 to 2) the end sequences of HindIII (C), BglII (D), and EcoRI (D) fragments can be unambiguously mapped to genomic <i>Igh</i> sequences. One representative 4C-seq experiment is shown for each viewpoint and cell type (C and D). (E) Annotation of the C57BL/6 Igh locus. The distinct V<sub>H</sub> gene families (different colors) in the distal, middle, and proximal V<sub>H</sub> gene regions (Johnston et al., 2006) as well as the D<sub>H</sub> (gray) and C<sub>H</sub> (blue) elements and Eµ and 3RR enhancers (red) in the 3 proximal Igh domain are shown together with the PAIR elements (orange) and the mm9 genomic coordinates of mouse chromosome 12. The indicated DNase I hypersensitive (DHS) regions and CTCF- and Pax5-binding sites were determined in Rag2<sup>/</sup> pro-B cells by paired-end sequencing and peak calling (MACS; p value &lt; 10<sup>10</sup>) (Ebert et al., 2011; Revilla-I-Domingo et al., 2012). See also Figure S1.</div>
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id="article-image-1"
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alt="Figure 2" />
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<strong class="figure-label">
<p> Figure 2. Loop Formation in the 3</p>
</strong>
</div>
</div>
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Figure 2. Loop Formation in the 3 Proximal <i> Igh </i> Region </p>
</strong>
<div class="figure-caption-contents"><p> (AC) 4C-seq interaction patterns revealed… </p></div>
</div>
<figcaption id="figure-caption-1" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Figure 2. Loop Formation in the 3 Proximal <i>Igh</i> Region
</strong>
<div class="figure-caption-contents">(AC) 4C-seq interaction patterns revealed by the indicated viewpoints (red) in short-term cultured <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> and <i>Rag2<sup>/</sup></i> pro-B cells. Vertical lines indicate the positions of relevant V<sub>H</sub>, D<sub>H</sub>, and C<sub>H</sub> gene segments as well as IGCR1, Eµ, and DNase I hypersensitive sites constituting the 3RR (HS1HS4) and 3CBE (HS5HS8) regions. Previously known and newly identified interactions are highlighted in green and orange, respectively. See legend of Figure 1 for further explanations. The data in (A) are based on average values of three independent experiments, and the results shown in (B) and (C) are derived from one experiment. (D) Characterization of the Cγ1-Cγ2b region. The sequences between the Cγ1 and Cγ2b gene segments were analyzed for binding of the indicated transcription factors and the presence of DHS sites and active histone modifications (H3K4me2 and H3K9ac) by deep sequencing of <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> (red) and <i>Rag2<sup>/</sup></i> (black) pro-B cells (Revilla-I-Domingo et al., 2012). See also Figure S2.</div>
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data-figure-id="F3">
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<strong class="figure-label">
<p> Figure 3. Local Interactions within the Distal… </p>
</strong>
</div>
</div>
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Figure 3. Local Interactions within the Distal V <sub> H </sub> Gene Cluster in the Absence of… </p>
</strong>
</div>
<figcaption id="figure-caption-2" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Figure 3. Local Interactions within the Distal V<sub>H</sub> Gene Cluster in the Absence of Locus Contraction
</strong>
<div class="figure-caption-contents">(A) 4C-seq interaction profiles at the <i>Igh</i> 5 end in cultured <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> and <i>Rag2<sup>/</sup></i> pro-B cells. Vertical lines indicate the positions of PAIR elements (yellow) and selected V<sub>H</sub> genes (blue). (B) 4C-seq interaction patterns detected with the indicated PAIR viewpoints (red) in the distal V<sub>H</sub> gene region. See legend of Figure 1 for further explanations. One 4C-seq experiment was performed with viewpoints Zfp386-HD and J558.88-ED, and the data of all other viewpoints are based on average values of three experiments. See also Figure S3.</div>
</figcaption>
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itemprop="contentUrl"
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data-figure-id="F4">
<img class="figure-thumb" itemprop="thumbnail"
id="article-image-3"
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alt="Figure 4" />
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<strong class="figure-label">
<p> Figure 4. Flexible Long-Range Interactions along the… </p>
</strong>
</div>
</div>
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Figure 4. Flexible Long-Range Interactions along the Distal V <sub> H </sub> Gene Region in the Presence… </p>
</strong>
</div>
<figcaption id="figure-caption-3" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Figure 4. Flexible Long-Range Interactions along the Distal V<sub>H</sub> Gene Region in the Presence of Locus Contraction
</strong>
<div class="figure-caption-contents">(AC) Long-range interactions of the indicated proximal viewpoints (red) with the distal V<sub>H</sub> gene region in cultured <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> and <i>Rag2<sup>/</sup></i> pro-B cells. See legend of Figure 1 for further explanations. The data of the HS3B-HD and Eµ-HD viewpoints (A) are average values of three experiments, and all other viewpoints (B, C) were analyzed once. (D) Comparison of the 4C-seq patterns obtained with random BAC libraries and <i>Rag2<sup>/</sup></i> pro-B cells (analyzed from HS3B-HD). The sequencing pattern of each BAC (with its size indicated below) was normalized by setting the highest peak to an RPM value of 10,000 (Figure S4B) prior to merging the patterns of the two BAC libraries (indicated in black and gray). Abbreviation: Del., internal BAC deletion. See also Figure S4.</div>
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<strong class="figure-label">
<p> Figure 5. Long-Range Interactions of the Distal… </p>
</strong>
</div>
</div>
<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Figure 5. Long-Range Interactions of the Distal V <sub> H </sub> Gene Region with the Proximal <i> Igh… </i> </p>
</strong>
</div>
<figcaption id="figure-caption-4" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Figure 5. Long-Range Interactions of the Distal V<sub>H</sub> Gene Region with the Proximal <i>Igh</i> Domain
</strong>
<div class="figure-caption-contents">(A) 4C-seq interaction pattern of PAIR8 with sequences across the <i>Igh</i> locus in cultured <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> and <i>Rag2<sup>/</sup></i> pro-B cells. (B) Long-range interactions of the indicated distal viewpoints (red) with sequences of the <i>Igh</i> 3 region in the indicated cultured pro-B cell types. See legends of Figures 1 and 2 for further explanations. The data of all viewpoints in (A) and (B) are average values of three experiments except for the PAIR4-HD analysis of <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i> pro-B cells (average of two experiments). (C) Comparison of the 4C-seq patterns between random BAC libraries and <i>Rag2<sup>/</sup></i> pro-B cells (analyzed from J558.89-HD). See legend of Figure 4D for normalization of the BAC sequencing pattern. Yellow shading denotes regions with a 4C-seq pattern that differs between the random BAC libraries and <i>Rag2<sup>/</sup></i> pro-B cells. The specificity of the 4C-seq interactions in the IGCR1/D<sub>H</sub> region (asterisk) of <i>Rag2<sup>/</sup></i> pro-B cells compared to the random BAC library was confirmed by 3C-qPCR (Figure S4E).</div>
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<p> Figure 6. Role of CTCF and 3</p>
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<p> Figure 6. Role of CTCF and 3 Regulatory Elements in Long-Range <i> Igh </i> Interactions </p>
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<div class="figure-caption-contents"><p> (A) 4C-seq… </p></div>
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Figure 6. Role of CTCF and 3 Regulatory Elements in Long-Range <i>Igh</i> Interactions
</strong>
<div class="figure-caption-contents">(A) 4C-seq analysis of cultured 129Sv pro-B cells of the indicated genotypes with the HS8-ED viewpoint (red). The homozygous J<sub>H</sub>T deletion eliminates the D<sub>H</sub>Q52, J<sub>H</sub>, and Eµ elements (Gu et al., 1993). The 129Sv sequence reads were mapped to genomic C57BL/6 sequences except for the available 129S1 <i>Igh</i> sequences (see Supplemental Experimental Procedures). A 120 kb deletion (Δ) was present in the E14 (129Ola) ESCs used to generate the J<sub>H</sub>T and 3RR mutant alleles. 4C-seq experiments were performed once with <i>Rag2<sup>/</sup></i> 3RR (/) mutant, <i>Rag2<sup>/</sup></i> Eµ (/) mutant, and J<sub>H</sub>T-deficient pro-B cells and twice with 129Sv <i>Rag2<sup>/</sup></i>, <i>Pax5<sup>/</sup>Rag2<sup>/</sup></i>, and <i>Rag2<sup>/</sup></i> IGCR1/CBE (/) mutant pro-B cells. (B) Two-color 3D DNA-FISH analysis with <i>Igh</i> BAC probes (indicated in A). Dot plots show the distances measured between the two DNA signals of individual <i>Igh</i> alleles together with the average distance determined for each genotype. (C) 3C-qPCR analysis of the IGCR1 interaction with distal PAIR4, PAIR8, and V<sub>H</sub>J558.89 sequences in cultured 129Sv pro-B cells of the indicated genotypes. A total of 12 3C templates of each genotype were used to determine the relative crosslinking frequency (see Supplemental Experimental Procedures), which was set to 1 for <i>Rag2<sup>/</sup></i> pro-B cells and is shown with the standard error of the mean. (D) Coprecipitation of CTCF with Pax5-Bio by streptavidin (SA) pull-down of nuclear extracts prepared from Abl-MLV-transformed pro-B cells of the <i>Pax5</i><sup>Bio/Bio</sup> (Pax5-Bio) or control <i>Rosa26</i><sup>BirA/BirA</sup> (BirA) genotype. The input (In; 1/100), supernatant (Sn; 1/100), and streptavidin-bound (B) precipitate were analyzed by immunoblotting (WB) with CTCF and Pax5 antibodies. (E) Coimmunoprecipitation of Pax5 from a nuclear extract of <i>Rag2<sup>/</sup></i> pro-B cells with CTCF antibodies followed by immunoblotting with a biotinylated rat anti-Pax5 mAb (detected with streptavidin-coupled horse radish peroxidase). Input (In; 1/100) and rabbit IgG were used as controls. Where indicated, DNA was digested with the endonuclease Benzonase during nuclear extract preparation. (F) Direct Pax5-CTCF protein interaction. The hexahistidine-tagged CTCF and GST-Pax5 proteins (schematically depicted to the right) were affinity purified from baculovirus-infected Sf9 cells (Figure S5B) and used for in vitro binding and GST pull-down assays followed by immunoblotting of the precipitates with CTCF and GST antibodies (see Supplemental Experimental Procedures). A protein size marker (in kilodaltons) and input (In; 1/20) are shown. Empty glutathione-sepharose beads () and GST-GFP were used as negative controls. Abbreviations are as follows: G, GST; P5, Pax5; PD, paired domain; OP, octapeptide; HD, partial homeodomain; TAD, transactivation domain; ID, inhibitory domain. See also Figure S5.</div>
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<p> Figure 7. YY1 Controls PAIR Function and… </p>
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<p> Figure 7. YY1 Controls PAIR Function and Long-Range Interactions across the <i> Igh </i> Locus </p>
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<div class="figure-caption-contents"><p> (A) 4C-seq… </p></div>
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<figcaption id="figure-caption-6" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
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Figure 7. YY1 Controls PAIR Function and Long-Range Interactions across the <i>Igh</i> Locus
</strong>
<div class="figure-caption-contents">(A) 4C-seq analysis of ex vivo sorted <i>Rag1</i><sup>Cre/+</sup><i>Yy1</i><sup>fl/fl</sup> pro-B cells (Figures S6B and S6C), control <i>Rag2<sup>/</sup></i> pro-B cells, and thymocytes with the viewpoint Eµ-HD (red). The Eµ-3CBE interaction is highlighted in orange. A red asterisk indicates the loss of D<sub>H</sub> sequences by D<sub>H</sub>-J<sub>H</sub> rearrangements in the recombination-proficient <i>Rag1</i><sup>Cre/+</sup><i>Yy1</i><sup>fl/fl</sup> pro-B cells. (B) Identification of YY1 peaks in the <i>Igh</i> locus by Bio-ChIP-sequencing of cultured pro-B cells from <i>Yy1</i><sup>ihCd2/+</sup><i>Rosa26</i><sup>BirA/BirA</sup><i>Rag2<sup>/</sup></i> mice. Vertical bars below the Bio-ChIP-seq track identify significant YY1 peaks that were called by MACS with a p value of &lt;10<sup>10</sup>. For comparison, the Pax5-binding and DHS site patterns of <i>Rag2<sup>/</sup></i> pro-B cells are shown (Revilla-I-Domingo et al., 2012). (C) YY1 binding at PAIR elements and associated V<sub>H</sub>3609 genes. (D and E) Analysis of YY1-dependent gene expression. The expression values (RPKM) of selected genes (D) and RNA-seq profiles of the antisense transcripts originating from PAIR4 and PAIR6 (E) are shown for <i>Rag1</i><sup>Cre/+</sup><i>Yy1</i><sup>fl/fl</sup> (red) and control <i>Rag1</i><sup>Cre/+</sup><i>Yy1</i><sup>fl/+</sup> (black) pro-B cells together with the standard error of the mean (based on two RNA-seq experiments for each genotype). See also Figure S6.</div>
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