{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T07:12:14Z","timestamp":1776409934806,"version":"3.51.2"},"reference-count":35,"publisher":"Proceedings of the National Academy of Sciences","issue":"23","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2011,6,7]]},"abstract":"<jats:p>\n            Compaction and looping of the ~2.5-Mb\n            <jats:italic>Igh<\/jats:italic>\n            locus during V(D)J rearrangement is essential to allow all V\n            <jats:sub>H<\/jats:sub>\n            genes to be brought in proximity with D\n            <jats:sub>H<\/jats:sub>\n            -J\n            <jats:sub>H<\/jats:sub>\n            segments to create a diverse antibody repertoire, but the proteins directly responsible for this are unknown. Because CCCTC-binding factor (CTCF) has been demonstrated to be involved in long-range chromosomal interactions, we hypothesized that CTCF may promote the contraction of the\n            <jats:italic>Igh<\/jats:italic>\n            locus. ChIP sequencing was performed on pro-B cells, revealing colocalization of CTCF and Rad21 binding at ~60 sites throughout the V\n            <jats:sub>H<\/jats:sub>\n            region and 2 other sites within the\n            <jats:italic>Igh<\/jats:italic>\n            locus. These numerous CTCF\/cohesin sites potentially form the bases of the multiloop rosette structures at the\n            <jats:italic>Igh<\/jats:italic>\n            locus that compact during Ig heavy chain rearrangement. To test whether CTCF was involved in locus compaction, we used 3D-FISH to measure compaction in pro-B cells transduced with CTCF shRNA retroviruses. Reduction of CTCF binding resulted in a decrease in\n            <jats:italic>Igh<\/jats:italic>\n            locus compaction. Long-range interactions within the\n            <jats:italic>Igh<\/jats:italic>\n            locus were measured with the chromosomal conformation capture assay, revealing direct interactions between CTCF sites 5\u2032 of\n            <jats:italic>DFL16<\/jats:italic>\n            and the 3\u2032 regulatory region, and also the intronic enhancer (E\u03bc), creating a D\n            <jats:sub>H<\/jats:sub>\n            -J\n            <jats:sub>H<\/jats:sub>\n            -E\u03bc-C\n            <jats:sub>H<\/jats:sub>\n            domain. Knockdown of CTCF also resulted in the increase of antisense transcription throughout the D\n            <jats:sub>H<\/jats:sub>\n            region and parts of the V\n            <jats:sub>H<\/jats:sub>\n            locus, suggesting a widespread regulatory role for CTCF. Together, our findings demonstrate that CTCF plays an important role in the 3D structure of the\n            <jats:italic>Igh<\/jats:italic>\n            locus and in the regulation of antisense germline transcription and that it contributes to the compaction of the\n            <jats:italic>Igh<\/jats:italic>\n            locus.\n          <\/jats:p>","DOI":"10.1073\/pnas.1019391108","type":"journal-article","created":{"date-parts":[[2011,5,24]],"date-time":"2011-05-24T04:31:06Z","timestamp":1306211466000},"page":"9566-9571","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":188,"title":["CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the\n            <i>Igh<\/i>\n            locus and antisense transcription in pro-B cells"],"prefix":"10.1073","volume":"108","author":[{"given":"Stephanie C.","family":"Degner","sequence":"first","affiliation":[{"name":"Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037;"}]},{"given":"Jiyoti","family":"Verma-Gaur","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037;"}]},{"given":"Timothy P.","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037;"}]},{"given":"Claudia","family":"Bossen","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093;"}]},{"given":"G. Michael","family":"Iverson","sequence":"additional","affiliation":[{"name":"Torrey Pines Institute for Molecular Studies, San Diego, CA 92121;"}]},{"given":"Ali","family":"Torkamani","sequence":"additional","affiliation":[{"name":"Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037;"}]},{"given":"Christian","family":"Vettermann","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and"}]},{"given":"Yin C.","family":"Lin","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093;"}]},{"given":"Zhongliang","family":"Ju","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461"}]},{"given":"Danae","family":"Schulz","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and"}]},{"given":"Caroline S.","family":"Murre","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093;"}]},{"given":"Barbara K.","family":"Birshtein","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461"}]},{"given":"Nicholas J.","family":"Schork","sequence":"additional","affiliation":[{"name":"Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037;"}]},{"given":"Mark S.","family":"Schlissel","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and"}]},{"given":"Roy","family":"Riblet","sequence":"additional","affiliation":[{"name":"Torrey Pines Institute for Molecular Studies, San Diego, CA 92121;"}]},{"given":"Cornelis","family":"Murre","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093;"}]},{"given":"Ann J.","family":"Feeney","sequence":"additional","affiliation":[{"name":"Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037;"}]}],"member":"341","published-online":{"date-parts":[[2011,5,23]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1126\/science.1068768","article-title":"Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development","volume":"296","author":"Kosak ST","year":"2002","unstructured":"ST Kosak, et al., Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296, 158\u2013162 (2002).","journal-title":"Science"},{"key":"e_1_3_4_2_2","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.cell.2008.03.024","article-title":"The 3D structure of the immunoglobulin heavy-chain locus: Implications for long-range genomic interactions","volume":"133","author":"Jhunjhunwala S","year":"2008","unstructured":"S Jhunjhunwala, et al., The 3D structure of the immunoglobulin heavy-chain locus: Implications for long-range genomic interactions. Cell 133, 265\u2013279 (2008).","journal-title":"Cell"},{"key":"e_1_3_4_3_2","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1101\/gad.1254305","article-title":"Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells","volume":"19","author":"Sayegh CE","year":"2005","unstructured":"CE Sayegh, S Jhunjhunwala, R Riblet, C Murre, Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells. Genes Dev 19, 322\u2013327, and correction (2008) 22:1717. (2005).","journal-title":"Genes Dev"},{"key":"e_1_3_4_4_2","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/ni1150","article-title":"Locus \u2018decontraction\u2019 and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene","volume":"6","author":"Rold\u00e1n E","year":"2005","unstructured":"E Rold\u00e1n, et al., Locus \u2018decontraction\u2019 and centromeric recruitment contribute to allelic exclusion of the immunoglobulin heavy-chain gene. Nat Immunol 6, 31\u201341 (2005).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_5_2","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1101\/gad.291504","article-title":"Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene","volume":"18","author":"Fuxa M","year":"2004","unstructured":"M Fuxa, et al., Pax5 induces V-to-DJ rearrangements and locus contraction of the immunoglobulin heavy-chain gene. Genes Dev 18, 411\u2013422 (2004).","journal-title":"Genes Dev"},{"key":"e_1_3_4_6_2","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1038\/ni.1626","article-title":"Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros","volume":"9","author":"Reynaud D","year":"2008","unstructured":"D Reynaud, et al., Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros. Nat Immunol 9, 927\u2013936 (2008).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_7_2","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1101\/gad.1529307","article-title":"Yin Yang 1 is a critical regulator of B-cell development","volume":"21","author":"Liu H","year":"2007","unstructured":"H Liu, et al., Yin Yang 1 is a critical regulator of B-cell development. Genes Dev 21, 1179\u20131189 (2007).","journal-title":"Genes Dev"},{"key":"e_1_3_4_8_2","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/ni876","article-title":"Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement","volume":"4","author":"Su IH","year":"2003","unstructured":"IH Su, et al., Ezh2 controls B cell development through histone H3 methylation and Igh rearrangement. Nat Immunol 4, 124\u2013131 (2003).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"44","DOI":"10.4049\/jimmunol.182.1.44","article-title":"Cutting edge: Developmental stage-specific recruitment of cohesin to CTCF sites throughout immunoglobulin loci during B lymphocyte development","volume":"182","author":"Degner SC","year":"2009","unstructured":"SC Degner, TP Wong, G Jankevicius, AJ Feeney, Cutting edge: Developmental stage-specific recruitment of cohesin to CTCF sites throughout immunoglobulin loci during B lymphocyte development. J Immunol 182, 44\u201348 (2009).","journal-title":"J Immunol"},{"key":"e_1_3_4_10_2","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.cell.2009.06.001","article-title":"CTCF: Master weaver of the genome","volume":"137","author":"Phillips JE","year":"2009","unstructured":"JE Phillips, VG Corces, CTCF: Master weaver of the genome. Cell 137, 1194\u20131211 (2009).","journal-title":"Cell"},{"key":"e_1_3_4_11_2","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.gde.2007.08.005","article-title":"We gather together: Insulators and genome organization","volume":"17","author":"Wallace JA","year":"2007","unstructured":"JA Wallace, G Felsenfeld, We gather together: Insulators and genome organization. Curr Opin Genet Dev 17, 400\u2013407 (2007).","journal-title":"Curr Opin Genet Dev"},{"key":"e_1_3_4_12_2","doi-asserted-by":"crossref","first-page":"10684","DOI":"10.1073\/pnas.0600326103","article-title":"CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2","volume":"103","author":"Kurukuti S","year":"2006","unstructured":"S Kurukuti, et al., CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. 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