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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

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

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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