This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T-Cell Receptor Beta Chain in Equus caballus
by
, ,
Rachele Antonacci
1,*,
Francesco Giannico
2
,
Roberta Moschetti
1,
Angela Pala
1,
Anna Caputi Jambrenghi
3 and
Serafina Massari
4 1
Department of Biosciences, Biotechnologies and Environment, University of Bari “Aldo Moro”, 70125 Bari, Italy
2
Department of Veterinary Medicine, University of Bari “Aldo Moro”, 70010 Bari, Italy
3
Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, 70126 Bari, Italy
4
Department of Biological and Environmental Science and Technologies, University of Salento, 73100 Lecce, Italy
*
Author to whom correspondence should be addressed.
Animals 2024, 14(19), 2817; https://doi.org/10.3390/ani14192817 (registering DOI)
Submission received: 6 August 2024
/
Revised: 4 September 2024
/
Accepted: 27 September 2024
/
Published: 29 September 2024
(This article belongs to the Special Issue Advances in Equine Genetics and Breeding)
Simple Summary
In the mammalian immune system, αβ T lymphocytes are a fundamental set of T cells capable of recognizing an extraordinary range of antigens, presented in the context of the major histocompatibility complex molecules. The function of αβ T cells is linked to the T-cell receptor, a heterodimeric cell surface protein composed of an α and β chain uniquely expressed on T cells. Unlike conventional proteins encoded by a single gene, α and β chains are encoded by a large set of noncontiguous TRA and TRB genes that are randomly assembled during a stochastic process known as V(D)J recombination, generating a large and diverse repertoire. The extent of diversification depends on the number of genes and their genomic organization at the TRA and TRB loci, which varies from species to species. In this paper, we describe the genomic organization and gene content of the horse TRB locus, based on the recently released horse genome. Compared to other mammalian species, the horse TRB locus was found to be the largest locus studied to date. A clonotype analysis of a transcriptomic dataset was also performed to assess the characteristics of the V(D)J somatic rearrangement. Overall, our data provide useful information for further functional studies in healthy and sick horses of different breeds.
Abstract
In this paper, we report a comprehensive and consistent annotation of the locus encoding the β-chain of the equine T-cell receptor (TRB), as inferred from recent genome assembly using bioinformatics tools. The horse TRB locus spans approximately 1 Mb, making it the largest locus among the mammalian species studied to date, with a significantly higher number of genes related to extensive duplicative events. In the region, 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ, and 2 TRBC genes, were identified. The general genomic organization resembles that of other mammals, with a V cluster of 135 TRBV genes located upstream of two in-tandem aligned TRBD-J-C clusters and an inverted TRBV gene at the 3′ end of the last TRBC gene. However, the horse b-chain repertoire would be affected by a high number of non-functional TRBV genes. Thus, we queried a transcriptomic dataset derived from splenic tissue of a healthy adult horse, using each TRBJ gene as a probe to analyze clonotypes encompassing the V(D)J junction. This analysis provided insights into the usage of the TRBV, TRBD, and TRBJ genes and the variability of the non-germline-encoded CDR3. Our results clearly demonstrated that the horse β-chain constitutes a complex level of variability, broadly like that described in other mammalian species.
Keywords:
alpha–beta T cell; TRB locus; Perissodactyla; Equus; equine genome; immunogenetics; evolution
