{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T16:37:22Z","timestamp":1790699842707,"version":"4.1.0"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,9,7]],"date-time":"2023-09-07T00:00:00Z","timestamp":1694044800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5\u2019D2-RS \u2013 3\u2019D1-RS. Identified rearrangements were in compliance with the classical 12\/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response.<\/jats:p>","DOI":"10.3389\/fimmu.2023.1245175","type":"journal-article","created":{"date-parts":[[2023,9,7]],"date-time":"2023-09-07T21:09:07Z","timestamp":1694120947000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity"],"prefix":"10.3389","volume":"14","author":[{"given":"Anastasia O.","family":"Smirnova","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna M.","family":"Miroshnichenkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laima D.","family":"Belyaeva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilya V.","family":"Kelmanson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri B.","family":"Lebedev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilgar Z.","family":"Mamedov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitriy M.","family":"Chudakov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander Y.","family":"Komkov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,9,7]]},"reference":[{"key":"B1","volume-title":"The T cell Receptor factsBook","author":"Lefranc","year":"2001"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2014.00022","article-title":"Immunoglobulin and T cell receptor genes: IMGT\u00ae and the birth and rise of immunoinformatics","volume":"5","author":"Lefranc","year":"2014","journal-title":"Front Immunol"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1038\/nri2941","article-title":"Recombination centres and the orchestration of V(D)J recombination","volume":"11","author":"Schatz","year":"2011","journal-title":"Nat Rev Immunol"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki010","article-title":"IMGT\/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes","volume":"33","author":"Giudicelli","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"B5","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1146\/annurev-genet-110410-132552","article-title":"V(D)J recombination: mechanisms of initiation","volume":"45","author":"Schatz","year":"2011","journal-title":"Annu Rev Genet"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1348","article-title":"The architecture of the 12RSS in V(D)J recombination signal and synaptic complexes","volume":"43","author":"Ciubotaru","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1038\/380085a0","article-title":"Initiation of V(D)J recombination in vitro obeying the 12\/23 rule","volume":"380","author":"Eastman","year":"1996","journal-title":"Nature"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1101\/gad.12.15.2305","article-title":"Enhancer control of V(D)J recombination at the TCRbeta locus: differential effects on DNA cleavage and joining","volume":"12","author":"Hempel","year":"1998","journal-title":"Genes Dev"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn553","article-title":"RAG2\u2019s non-core domain contributes to the ordered regulation of V(D)J recombination","volume":"36","author":"Curry","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1038\/330722a0","article-title":"T-cell receptor delta gene rearrangements in early thymocytes","volume":"330","author":"Chien","year":"1987","journal-title":"Nature"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1182\/blood.V75.9.1834.1834","article-title":"High prevalence of T-cell receptor V\u03b42-(D)-D\u03b43 or D\u03b41\/2-D\u03b43 rearrangements in B-precursor acute lymphoblastic leukemias","volume":"75","author":"Biondi","year":"1990","journal-title":"Blood"},{"key":"B12","volume-title":"Kuby Immunology","author":"Punt","year":"2019"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1101\/gr.259598.119","article-title":"V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s","volume":"30","author":"Safonova","year":"2020","journal-title":"Genome Res"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1007\/s13238-014-0060-1","article-title":"Characterization of human \u03b1\u03b2TCR repertoire and discovery of D-D fusion in TCR\u03b2 chains","volume":"5","author":"Liu","year":"2014","journal-title":"Protein Cell"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005572","article-title":"Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires","volume":"13","author":"Pogorelyy","year":"2017","journal-title":"PloS Comput Biol"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-065X.2000.imr017518.x","article-title":"Terminal deoxynucleotidyl transferase and repertoire development","volume":"175","author":"Benedict","year":"2000","journal-title":"Immunol Rev"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.970285","article-title":"Inactivated tick-borne encephalitis vaccine elicits several overlapping waves of T cell response","volume":"13","author":"Sycheva","year":"2022","journal-title":"Front Immunol"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006874","article-title":"Genesis of the \u03b1\u03b2 T-cell receptor","volume":"15","author":"Dupic","year":"2019","journal-title":"PloS Comput Biol"},{"key":"B19","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1038\/s41467-018-02832-w","article-title":"High-throughput immune repertoire analysis with IGoR","volume":"9","author":"Marcou","year":"2018","journal-title":"Nat Commun"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.33050","article-title":"Method for identification of condition-associated public antigen receptor sequences","volume":"7","author":"Pogorelyy","year":"2018","journal-title":"Elife"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000314","article-title":"Detecting T cell receptors involved in immune responses from single repertoire snapshots","volume":"17","author":"Pogorelyy","year":"2019","journal-title":"PloS Biol"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.00299","article-title":"Shorter TCR \u03b2-chains are highly enriched during thymic selection and antigen-driven selection","volume":"10","author":"Hou","year":"2019","journal-title":"Front Immunol"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2104367118","article-title":"TCR\u03b2 rearrangements without a D segment are common, abundant, and public","volume":"118","author":"de Greef","year":"2021","journal-title":"Proc Natl Acad Sci"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1038\/bmt.2016.148","article-title":"Reliability of immune receptor rearrangements as genetic markers for minimal residual disease monitoring","volume":"51","author":"Nazarov","year":"2016","journal-title":"Bone Marrow Transplant"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1038\/s41375-019-0496-7","article-title":"Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study","volume":"33","author":"Br\u00fcggemann","year":"2019","journal-title":"Leukemia"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1182\/blood.2021015036","article-title":"Epigenetic regulator genes direct lineage switching in MLL\/AF4 leukaemia","volume":"140","author":"Tirtakusuma","year":"2022","journal-title":"Blood"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23074019","article-title":"Lineage conversion in pediatric B-cell precursor acute leukemia under blinatumomab therapy","volume":"23","author":"Semchenkova","year":"2022","journal-title":"Int J Mol Sci"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1111\/bjh.16230","article-title":"High-throughput sequencing of T-cell receptor alpha chain clonal rearrangements at the DNA level in lymphoid Malignancies","volume":"188","author":"Komkov","year":"2020","journal-title":"Br J Haematol"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3364","article-title":"MiXCR: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat Methods"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004503","article-title":"VDJtools: unifying post-analysis of T cell receptor repertoires","volume":"11","author":"Shugay","year":"2015","journal-title":"PloS Comput Biol"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1101\/gr.849004","article-title":"WebLogo: A sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.69157","article-title":"The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling","volume":"12","author":"Smirnova","year":"2023","journal-title":"Elife"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2023.1245175\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,7]],"date-time":"2023-09-07T21:09:11Z","timestamp":1694120951000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2023.1245175\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,7]]},"references-count":33,"alternative-id":["10.3389\/fimmu.2023.1245175"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2023.1245175","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9,7]]},"article-number":"1245175"}}