Measuring CDR3 length variability in individuals during ontogeny

Desravines, Soléenne; Hsu, Ellen

doi:10.1016/0022-1759(94)90058-2

Cited by 13 publications

(9 citation statements)

References 14 publications

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“…This is somewhat longer than mouse (2-19 codons, mean 8.7 codons) (34) and Xenopus (3-12 codons, mean 8.6 codons) (35), whose respective major L chain isotypes are and rho, as described above. The greater length of the average shark H chain CDR3 certainly is a result of rearrangement of the two germline D gene segments per locus, and perhaps one might speculate about a more prominent role for CDR3, in H or L chain, when there is only one V H gene family in nurse shark (33) and other elasmobranchs (3).…”

Section: Cdr3 Diversitymentioning

confidence: 74%

Shark Ig Light Chain Junctions Are as Diverse as in Heavy Chains

Fleurant

Changchien

Chen

et al. 2004

The Journal of Immunology

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We have characterized a small family of four genes encoding one of the three nurse shark Ig L chain isotypes, called NS5. All NS5 cDNA sequences are encoded by three loci, of which two are organized as conventional clusters, each consisting of a V and J gene segment that can recombine and one C region exon; the third contains a germline-joined VJ in-frame and the fourth locus is a pseudogene. This is the second nurse shark L chain type where both germline-joined and split V-J organizations have been found. Since there are only two rearranging Ig loci, it was possible for the first time to examine junctional diversity in defined fish Ig genes, comparing productive vs nonproductive rearrangements. N region addition was found to be considerably more extensive in length and in frequency than any other vertebrate L chain so far reported and rivals that in H chain. We put forth the speculation that the unprecedented efficiency of N region addition (87–93% of NS5 sequences) may be a result not only of simultaneous H and L chain rearrangement in the shark but also of processing events that afford greater accessibility of the V or J gene coding ends to terminal deoxynucleotidyltransferase.

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Section: Cdr3 Diversitymentioning

confidence: 74%

Shark Ig Light Chain Junctions Are as Diverse as in Heavy Chains

Fleurant

Changchien

Chen

et al. 2004

The Journal of Immunology

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“…In-frame rearrangements can be distinguished from nonproductive, out-of-frame rearrangements by using PCR run-off assays as described previously (28,29) and by using an oligonucleotide designed to assay all VJ L CDR3 sequences independent of whether they had undergone sequence divergence by gene conversion. Selection for inframe VJ L junctions was observed clearly in the ϩ L ϩ populations from RCAS-T-infected chicks with two bands, separated in size by 3 nt, dominating the VJ L junctions (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Five-microliter aliquots of the reaction were run on sequencing gels as described elsewhere (28,29).…”

mentioning

confidence: 99%

Development of B cells expressing surface immunoglobulin molecules that lack V(D)J-encoded determinants in the avian embryo bursa of Fabricius

Sayegh

Demaries

Iacampo

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

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Immunoglobulin gene rearrangement in avian B cell precursors generates surface Ig receptors of limited diversity. It has been proposed that specificities encoded by these receptors play a critical role in B lineage development by recognizing endogenous ligands within the bursa of Fabricius. To address this issue directly we have introduced a truncated surface IgM, lacking variable region domains, into developing B precursors by retroviral gene transfer in vivo. Cells expressing this truncated receptor lack endogenous surface IgM, and the low level of endogenous Ig rearrangements that have occurred within this population of cells has not been selected for having a productive reading frame. Such cells proliferate rapidly within bursal epithelial buds of normal morphology. In addition, despite reduced levels of endogenous light chain rearrangement, those light chain rearrangements that have occurred have undergone variable region diversification by gene conversion. Therefore, although surface expression of an Ig receptor is required for bursal colonization and the induction of gene conversion, the specificity encoded by the prediversified receptor is irrelevant and, consequently, there is no obligate ligand for V(D)Jencoded determinants of prediversified avian cell surface IgM receptor.The rearrangement of chicken Ig genes generates minimal antibody diversity. At the light chain (L) locus, the unique, functional V L 1 gene rearranges to the unique J L segment in all B cells (1). Similarly, at the heavy chain (H) locus, unique V H 1 and J H genes undergo rearrangement with a family of highly conserved D H elements to form a VDJ H complex of limited diversity (2, 3). Junctional diversity is limited further because of the lack of N nucleotide additions in chicken V(D)J junctions (4). A diverse repertoire of B cell specificities is generated by somatic gene-conversion events in which VD H and V L sequences in functionally rearranged VDJ H and VJ L genes are replaced by homologous sequences from upstream V L and V H pseudogenes (⌿V L and ⌿V H ) (2, 5-7).The bursa of Fabricius is the primary site of B cell lymphopoiesis in avian species, and surgical or chemical ablation of the chicken bursa profoundly disrupts the normal progression of B cell development and the generation of diversity by gene conversion (reviewed in refs. 7-10). The bursa is colonized by a single wave of B cell precursors during embryogenesis starting at about embryonic day 8 (E8) and lasting about a week (11). Within the bursa, B cell precursors first are observed in the mesenchymal tissue, and 20,000-40,000 precursors subsequently migrate across the bursal epithelial basement membrane and begin to proliferate in oligoclonal clusters or epithelial buds from which the discrete follicles of the mature bursa are derived (12, 13).Surface Ig (sIg) ϩ B cell precursors first are observed by about E9-E10, and the frequency of such cells increases rapidly during the embryonic period (14). Although Ig gene rearrangement is not intrinsically biased towar...

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“…While no tool such as monoclonal antibodies to T cell marker(s) was available in this model, this approach demonstrated that fish could mount specific T cell responses against virus, which could be found in all individuals (public clonotypes) or not (private clonotypes). Similar strategies, developed by other groups (81) and following the same approach in parallel, analyzed the IG repertoire in Xenopus at different stages of development, describing a more restricted IG junction diversity in the tadpole compared to the adult.…”

Section: Methods Developed To Describe the Ig And Tr Repertoiresmentioning

confidence: 99%

The Past, Present, and Future of Immune Repertoire Biology – The Rise of Next-Generation Repertoire Analysis

et al. 2013

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T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a “next-generation” of repertoire analysis.

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Measuring CDR3 length variability in individuals during ontogeny

Cited by 13 publications

References 14 publications

Shark Ig Light Chain Junctions Are as Diverse as in Heavy Chains

Shark Ig Light Chain Junctions Are as Diverse as in Heavy Chains

Development of B cells expressing surface immunoglobulin molecules that lack V(D)J-encoded determinants in the avian embryo bursa of Fabricius

The Past, Present, and Future of Immune Repertoire Biology – The Rise of Next-Generation Repertoire Analysis

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