Germline DNA Retention in Murine and Human Rearranged T Cell Receptor Gene Coding Joints: Alternative Recombination Signal Sequences and V(D)J Recombinase Errors

Justyna Mika, Sylwia Kabacik, Christophe Badie, Joanna Polanska, Serge M. Candéias*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The genes coding for the antigenic T cell receptor (TR) subunits are assembled in thymocytes from discrete V, D, and J genes by a site-specific recombination process. A tight control of this activity is required to prevent potentially detrimental recombination events. V, D, and J genes are flanked by semi-conserved nucleotide motives called recombination signal sequences (RSSs). V(D)J recombination is initiated by the precise introduction of a DNA double-strand break exactly at the border of the genes and their RSSs by the RAG recombinase. RSSs are therefore physically separated from the coding region of the genes before assembly of a rearranged TR gene. During a high throughput profiling of TRB genes in mice, we identified rearranged TRB genes in which part or all of a flanking RSS was retained in V-D or D-J coding joints. In some instances, this retention of germline DNA resulted from the use of an upstream alternative RSS. However, we also identified TRB sequences where retention of germline DNA occurred in the absence of alternative RSS, suggesting that RAG activity was mis-targeted during recombination. Similar events were also identified in human rearranged TRB and TRG genes. The use of alternative RSSs during V(D)J recombination illustrates the complexity of RAG-RSSs interactions during V(D)J recombination. While the frequency of errors resulting from mis-targeted RAG activity is very low, we believe that these RAG errors may be at the origin of oncogenic translocations and are a threat for genetic stability in developing lymphocytes.

Original languageEnglish
Article number2637
JournalFrontiers in Immunology
Publication statusPublished - 8 Nov 2019

Bibliographical note

Funding Information:
The authors want to thank Drs. H. Robins, O. Pearson, and D. E. Hamm (Adaptive Biotechnologies) for making available the datasets of rearranged TRB and TRG genes, and Dr. T. Rabilloud for critical reading of the manuscript. Funding. This work has been supported by the European Commissions [DoReMi, European Atomic Energy Community's Seventh Framework Program (FP7/2007?2011) under Grant Agreement No. 249689], in part through the European Social Fund grant POWR.03.02.00-00-I029 (JM), and the Polish National Science Centre grant OPUS no. 2015/19/B/ST6/01736 and Silesian University of Technology grant no. 02/010/BK19/0143 (JP). Calculations were carried out using infrastructure of GeCONiI (POIG.02.03.01-24-099/13).


  • RSS
  • T cell receptor genes
  • V(D)J recombination
  • errors
  • lymphoid neoplasms
  • translocations


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