{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:40:24Z","timestamp":1768506024776,"version":"3.49.0"},"posted":{"date-parts":[[2023,4,25]]},"group-title":"Immunology","reference-count":56,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,4,25]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Immunoglobulin heavy chain variable region exons are assembled in progenitor-B cells, from V\n                  <jats:sub>H<\/jats:sub>\n                  , D, and J\n                  <jats:sub>H<\/jats:sub>\n                  gene segments located in separate clusters across the\n                  <jats:italic>Igh<\/jats:italic>\n                  locus. RAG endonuclease initiates V(D)J recombination from a J\n                  <jats:sub>H<\/jats:sub>\n                  -based recombination center (RC). Cohesin-mediated extrusion of upstream chromatin past RC-bound RAG presents Ds for joining to J\n                  <jats:sub>H<\/jats:sub>\n                  s to form a DJ\n                  <jats:sub>H<\/jats:sub>\n                  -RC.\n                  <jats:italic>Igh<\/jats:italic>\n                  has a provocative number and organization of CTCF-binding-elements (CBEs) that can impede loop extrusion. Thus,\n                  <jats:italic>Igh<\/jats:italic>\n                  has two divergently oriented CBEs (CBE1 and CBE2) in the IGCR1 element between the V\n                  <jats:sub>H<\/jats:sub>\n                  and D\/J\n                  <jats:sub>H<\/jats:sub>\n                  domains, over 100 CBEs across the V\n                  <jats:sub>H<\/jats:sub>\n                  domain convergent to CBE1, and 10 clustered 3\u2019\n                  <jats:italic>Igh<\/jats:italic>\n                  -CBEs convergent to CBE2 and V\n                  <jats:sub>H<\/jats:sub>\n                  CBEs. IGCR1 CBEs segregate D\/J\n                  <jats:sub>H<\/jats:sub>\n                  and V\n                  <jats:sub>H<\/jats:sub>\n                  domains by impeding loop extrusion-mediated RAG-scanning. Down-regulation of WAPL, a cohesin unloader, in progenitor-B cells neutralizes CBEs, allowing DJ\n                  <jats:sub>H<\/jats:sub>\n                  -RC-bound RAG to scan the VH domain and perform VH-to-DJH rearrangements. To elucidate potential roles of IGCR1-based CBEs and 3\u2019\n                  <jats:italic>Igh<\/jats:italic>\n                  -CBEs in regulating RAG-scanning and elucidate the mechanism of the \u201cordered\u201d transition from D-to-J\n                  <jats:sub>H<\/jats:sub>\n                  to V\n                  <jats:sub>H<\/jats:sub>\n                  -to-DJ\n                  <jats:sub>H<\/jats:sub>\n                  recombination, we tested effects of deleting or inverting IGCR1 or 3\u2019\n                  <jats:italic>Igh<\/jats:italic>\n                  -CBEs in mice and\/or progenitor-B cell lines. These studies revealed that normal IGCR1 CBE orientation augments RAG-scanning impediment activity and suggest that 3\u2019\n                  <jats:italic>Igh<\/jats:italic>\n                  -CBEs reinforce ability of the RC to function as a dynamic loop extrusion impediment to promote optimal RAG scanning activity. Finally, our findings indicate that ordered V(D)J recombination can be explained by a gradual WAPL down-regulation mechanism in progenitor B cells as opposed to a strict developmental switch.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>SIGNIFICANCE STATEMENT<\/jats:title>\n                  <jats:p>To counteract diverse pathogens, vertebrates evolved adaptive immunity to generate diverse antibody repertoires through a B lymphocyte-specific somatic gene rearrangement process termed V(D)J recombination. Tight regulation of the V(D)J recombination process is vital to generating antibody diversity and preventing off-target activities that can predispose the oncogenic translocations. Recent studies have demonstrated V(D)J rearrangement is driven by cohesin-mediated chromatin loop extrusion, a process that establishes genomic loop domains by extruding chromatin, predominantly, between convergently-oriented CTCF looping factor-binding elements (CBEs). By deleting and inverting CBEs within a critical antibody heavy chain gene locus developmental control region and a loop extrusion chromatin-anchor at the downstream end of this locus, we reveal how these elements developmentally contribute to generation of diverse antibody repertoires.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.04.21.537836","type":"posted-content","created":{"date-parts":[[2023,4,25]],"date-time":"2023-04-25T17:40:17Z","timestamp":1682444417000},"source":"Crossref","is-referenced-by-count":0,"title":["Contribution of the IGCR1 regulatory element and the 3\n                  <i>\u2019Igh<\/i>\n                  CBEs to Regulation of\n                  <i>Igh<\/i>\n                  V(D)J Recombination"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1622-524X","authenticated-orcid":false,"given":"Zhuoyi","family":"Liang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lijuan","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Yongxin Ye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sherry G.","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiwen","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunguang","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hai-Qiang","family":"Dai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhaoqing","family":"Ba","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederick W.","family":"Alt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023042800400593000_2023.04.21.537836v1.1","doi-asserted-by":"crossref","unstructured":"Y. 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