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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Opsin 3, encoding a non-visual photoreceptor, is a pseudogene in cattle.

Erina Kachi1, Kei Kazama1, Masaru Murakami1

  • 1Azabu University, Graduate School of Veterinary Medicine, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5201, Japan.

Research in Veterinary Science
|February 22, 2025
PubMed
Summary

The non-visual photoreceptor opsin 3 (OPN3) gene is pseudogenic in cattle and goats, meaning it does not produce a functional protein. This study found no evidence of OPN3 expression in various bovine tissues.

Keywords:
CattleG protein-coupled receptorNon-visual opsinOpsin 3PseudogeneStop codon

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Area of Science:

  • Molecular Biology
  • Genetics
  • Photoreceptor Research

Background:

  • Non-visual opsin 3 (OPN3) is a light-sensing G protein-coupled receptor involved in thermogenesis.
  • OPN3 expression is documented in various mammalian tissues, but its presence in ruminants is poorly understood.
  • Previous data suggested a predicted bovine OPN3 mRNA sequence, necessitating experimental verification.

Purpose of the Study:

  • To investigate the expression and integrity of the opsin 3 (OPN3) gene in cattle.
  • To determine if OPN3 is functional in bovines and related species within Cetartiodactyla.

Main Methods:

  • Reverse transcription PCR (RT-PCR) was used to detect OPN3 mRNA in various bovine tissues, including retina, testis, and placenta.
  • RNA sequencing was performed on bovine placenta.
  • Direct genomic DNA sequencing was employed to analyze the OPN3 gene sequence.

Main Results:

  • No amplified OPN3 PCR products were detected in any of the eleven bovine tissues examined.
  • OPN3 was expressed in mouse and horse testes but not in cattle or goat tissues.
  • Genomic sequencing revealed a premature stop codon in the bovine OPN3 sequence, indicating it is a pseudogene.

Conclusions:

  • Bovine OPN3 is pseudogenic, lacking the ability to encode a complete functional receptor protein.
  • The OPN3 gene is also likely pseudogenic in other Cetartiodactyla, such as goats.
  • This finding has implications for understanding light-sensing pathways and thermoregulation in ruminants.