Violation of the 12/23 rule of genomic V(D)J recombination is common in lymphocytes
- Nicholas J. Parkinson1,
- Matthew Roddis1,
- Ben Ferneyhough1,
- Gang Zhang1,
- Adam J. Marsden1,
- Siarhei Maslau1,2,
- Yasmin Sanchez-Pearson1,
- Thomas Barthlott3,
- Ian R. Humphreys4,
- Kristin Ladell4,
- David A. Price4,5,
- Chris P. Ponting2,
- Georg Hollander3,6 and
- Michael D. Fischer1,7
- 1Systems Biology Laboratory UK, Abingdon, Oxfordshire OX14 4SA, United Kingdom;
- 2MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom;
- 3Paediatric Immunology, Department of Biomedicine, University of Basel and The Basel University Children’s Hospital, 4058 Basel, Switzerland;
- 4Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom;
- 5Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 6Developmental Immunology, Weatherall Institute of Molecular Medicine and Department of Paediatrics, University of Oxford, Oxford OX3 9DS, United Kingdom;
- 7Department of Oncology, Division of Cellular and Molecular Medicine, St. George’s, University of London, London SW17 0QT, United Kingdom
- Corresponding author: nickp{at}sbl-uk.org
Abstract
V(D)J genomic recombination joins single gene segments to encode an extensive repertoire of antigen receptor specificities in T and B lymphocytes. This process initiates with double-stranded breaks adjacent to conserved recombination signal sequences that contain either 12- or 23-nucleotide spacer regions. Only recombination between signal sequences with unequal spacers results in productive coding genes, a phenomenon known as the “12/23 rule.” Here we present two novel genomic tools that allow the capture and analysis of immune locus rearrangements from whole thymic and splenic tissues using second-generation sequencing. Further, we provide strong evidence that the 12/23 rule of genomic recombination is frequently violated under physiological conditions, resulting in unanticipated hybrid recombinations in ∼10% of Tcra excision circles. Hence, we demonstrate that strict adherence to the 12/23 rule is intrinsic neither to recombination signal sequences nor to the catalytic process of recombination and propose that nonclassical excision circles are liberated during the formation of antigen receptor diversity.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.179770.114.
Freely available online through the Genome Research Open Access option.
- Received June 12, 2014.
- Accepted October 31, 2014.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0.
