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Animals : an open access journal from MDPI2024; 14(19); 2817; doi: 10.3390/ani14192817

A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T-Cell Receptor Beta Chain in Equus caballus.

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.
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Publication Date: 2024-09-29 PubMed ID: 39409766PubMed Central: PMC11475548DOI: 10.3390/ani14192817Google Scholar: Lookup
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Summary

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The research paper presents a detailed examination of the locus encoding the β-chain of the equine T-cell receptor (TRB). It reports that the horse TRB locus is the largest among mammalian species studied so far and has a high number of genes due to extensive duplication events.

Examination of the TRB Locus

  • The researchers looked at the locus encoding the β-chain of the equine T-cell receptor using recent genome assembly and bioinformatics tools.
  • The equine T-cell receptor β-chain locus is approximately 1 Mb, making it the largest locus among the mammalian species that have been studied so far.

Genes Identified in the Locus

  • Within this locus, the study identified 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ, and 2 TRBC genes.
  • Due to extensive duplication events, this particular locus has a significantly higher number of genes.

Genomic Organization

  • The genomic organization of this locus is similar to that observed in other mammals. It has a V cluster of 135 TRBV genes located upstream of two in-tandem aligned TRBD-J-C clusters.
  • The study notes, however, that there is an inverted TRBV gene at the 3′ end of the last TRBC gene.

Non-functional TRBV Genes

  • The β-chain repertoire in horses is affected by a high number of non-functional TRBV genes.
  • By analyzing the transcriptomic dataset of the splenic tissue from a healthy adult horse using each TRBJ gene, the researchers studied clonotypes covering the V(D)J junction.

Levels of Variability

  • This analysis helped provide insights into the use of TRBV, TRBD, and TRBJ genes, as well as the variability of the non-germline-encoded CDR3.
  • Despite its complexity, the levels of variability in the horse β-chain are broadly similar to those found in other mammalian species as per the findings of the study.

Cite This Article

APA
(2024). A Comprehensive Analysis of the Genomic and Expressed Repertoire of the T-Cell Receptor Beta Chain in Equus caballus. Animals (Basel), 14(19), 2817. https://doi.org/10.3390/ani14192817

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 14
Issue: 19
PII: 2817

Researcher Affiliations

Conflict of Interest Statement

The authors declare no conflicts of interest.

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