Abundance, efficiency, and stability of reference transcript expression in a seasonal rodent: The Siberian hamster

Stewart, C., Liddle, T. A. and Stevenson, T. J. (2022) Abundance, efficiency, and stability of reference transcript expression in a seasonal rodent: The Siberian hamster. PLoS ONE, 17(10), e0275263. (doi: 10.1371/journal.pone.0275263) (PMID:36190976) (PMCID:PMC9529152)

Abstract

Quantitative PCR (qPCR) is a common molecular tool to analyse the expression of transcripts in non-traditional animal models. Most animals experience tissue-specific seasonal changes in cell structure, growth, and cellular function. As a consequence, the choice of reference or ‘house-keeping’ genes is essential to standardize expression levels of target transcripts of interest for qPCR analyses. This study aimed to determine the abundance, efficiency and stability of several reference genes commonly used for normalisation of qPCR analyses in a model of seasonal biology: the Siberian hamster (Phodopus sungorus). Liver, brown-adipose tissue (BAT), white adipose tissue (WAT), testes, spleen, kidney, the hypothalamic arcuate nucleus, and the pituitary gland from either long or short photoperiod Siberian hamsters were dissected to test tissue-specific and photoperiod effects on reference transcripts. qPCR was conducted for common reference genes including 18s ribosomal RNA (18s), glyceraldehyde 3-phosphate dehydrogenase (Gapdh), hypoxanthine-guanine phosphoribosyltransferase (Hprt), and actin-β (Act). Cycling time (Ct), efficiency (E) and replicate variation of Ct and E measured by percent coefficient of variance (CV%) was determined using PCR miner. Measures of stability were assessed using a combined approach of NormFinder and BestKeeper. 18s and Act did not vary in Ct across photoperiod conditions. Splenic, WAT and BAT Gapdh Ct was higher in long compared to short photoperiod. Splenic Hprt Ct was higher in long photoperiods. There was no significant effect of photoperiod, tissue or interaction on measures of efficiency, Ct CV%, or efficiency CV%. NormFinder and BestKeeper confirmed that 18s, Gapdh and Hprt were highly stable, while Act showed low stability. These findings suggest that 18s and Hprt show the most reliable stability, efficiency, and abundance across the tissues. Overall, the study provides a comprehensive and standardised approach to assess multiple reference genes in the Siberian hamster and help to inform molecular assays used in studies of photoperiodism.

• Item Type: Articles
• Additional Information: This work was funded by the Leverhulme Trust (https://www.leverhulme.ac.uk/) Research Leader Award to TJS (LT-2019-006).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Liddle, Adam and Stewart, Calum and Stevenson, Professor Tyler

Creator Roles

Stewart, C.: Investigation, Methodology, Writing – review and editing
Liddle, T. A.: Writing – original draft
Stevenson, T. J.: Conceptualization, Writing – review and editing

• Authors: Stewart, C., Liddle, T. A., and Stevenson, T. J.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: PLoS ONE
• Publisher: Public Library of Science
• ISSN: 1932-6203
• ISSN (Online): 1932-6203
• Published Online: 03 October 2022
• Copyright Holders: Copyright © 2022 Stewart et al
• First Published: First published in PLoS ONE 17(10):e0275263
• Publisher Policy: Reproduced under a Creative Commons license