Palindromic nucleotide analysis in human T cell receptor rearrangements.

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 ba...

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Autores principales:	Santosh K Srivastava, Harlan S Robins
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b36fcf249e804073ae82b1aec5ad180c
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spelling	oai:doaj.org-article:b36fcf249e804073ae82b1aec5ad180c2021-11-18T08:03:57ZPalindromic nucleotide analysis in human T cell receptor rearrangements.1932-620310.1371/journal.pone.0052250https://doaj.org/article/b36fcf249e804073ae82b1aec5ad180c2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284955/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Diversity 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.Santosh K SrivastavaHarlan S RobinsPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e52250 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Santosh K Srivastava Harlan S Robins Palindromic nucleotide analysis in human T cell receptor rearrangements.
description	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.
format	article
author	Santosh K Srivastava Harlan S Robins
author_facet	Santosh K Srivastava Harlan S Robins
author_sort	Santosh K Srivastava
title	Palindromic nucleotide analysis in human T cell receptor rearrangements.
title_short	Palindromic nucleotide analysis in human T cell receptor rearrangements.
title_full	Palindromic nucleotide analysis in human T cell receptor rearrangements.
title_fullStr	Palindromic nucleotide analysis in human T cell receptor rearrangements.
title_full_unstemmed	Palindromic nucleotide analysis in human T cell receptor rearrangements.
title_sort	palindromic nucleotide analysis in human t cell receptor rearrangements.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/b36fcf249e804073ae82b1aec5ad180c
work_keys_str_mv	AT santoshksrivastava palindromicnucleotideanalysisinhumantcellreceptorrearrangements AT harlansrobins palindromicnucleotideanalysisinhumantcellreceptorrearrangements
_version_	1718422308004036608

Palindromic nucleotide analysis in human T cell receptor rearrangements.

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