ArticlePloS one2012
Palindromic nucleotide analysis in human T cell receptor rearrangements.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
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- The recombinase activating genes: architects of immune diversity during lymphocyte development.Frontiers in immunology · 2023Review
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- Reconstituting T cell receptor selection in-silico.Genes and immunity · 2021Article
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- Immunotherapy and molecular role of T-cell in PD-1 antibody treated resectable lung cancer patients.Journal of thoracic disease · 2018Article
- Immune Escape in Breast Cancer DuringCancer discovery · 2017Article
- Tumor- and Neoantigen-Reactive T-cell Receptors Can Be Identified Based on Their Frequency in Fresh Tumor.Cancer immunology research · 2016Article
- CDR3 motif generation and selection in the BV19-utilizing subset of the human CD8 T cell repertoire.Molecular immunology · 2016Article
- Illegitimate V(D)J recombination-mediated deletions in Notch1 and Bcl11b are not sufficient for extensive clonal expansion and show minimal age or sex bias in frequency or junctional processing.Mutation research · 2014Article
- The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis.Frontiers in immunology · 2013Review
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Diversity of T cell receptor (TCR) genes is primarily generated by nucleotide insertions upon rearrangement from their germ line-encoded V, D and J segments. Nucleotide insertions at V-D and D-J junctions are random, but some small subsets of these insertions are exceptional, in that one to three base pairs inversely repeat the sequence of the germline DNA. These short complementary palindromic sequences are called P nucleotides. We apply the ImmunoSeq deep-sequencing assay to the third complementarity determining region (CDR3) of the β chain of T cell receptors, and use the resulting data to study P nucleotides in the repertoire of naïve and memory CD8(+) and CD4(+) T cells. We estimate P nucleotide distributions in a cross section of healthy adults and different T cell subtypes. We show that P nucleotide frequency in all T cell subtypes ranges from 1% to 2%, and that the distribution is highly biased with respect to the coding end of the gene segment. Classification of observed palindromic sequences into P nucleotides using a maximum conditional probability model shows that single base P nucleotides are very rare in VDJ recombination; P nucleotides are primarily two bases long. To explore the role of P nucleotides in thymic selection, we compare P nucleotides in productive and non-productive sequences of CD8(+) naïve T cells. The naïve CD8(+) T cell clones with P nucleotides are more highly expanded.
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