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CC BY V4.0, Open Access
Journal article
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)
G3 : genes - genomes - genetics, Vol.12(3)
03/04/2022
PMID: 35100340
Abstract
Understanding hibernation in brown bears (Ursus arctos) can provide insight into some human diseases. During hibernation, brown bears experience periods of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic aspects of human diseases such as type 2 diabetes, muscle atrophy, as well as renal and heart failure. The reversibility of these states from hibernation to active season enables the identification of mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons in bears. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, full-length RNA-sequencing (Iso-Seq) was performed on adipose, skeletal muscle, and liver from three individual bears sampled during both active and hibernation seasons. The existing reference genome annotation was improved by combining it with the Iso-Seq data. Short-read RNA-sequencing data from six individuals were mapped to the new reference annotation to quantify differential isoform usage (DIU) between tissues and seasons. We identified differentially expressed isoforms in all three tissues, to varying degrees. Adipose had a high level of DIU with isoform switching, regardless of whether the genes were differentially expressed. Our analyses revealed that DIU, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.
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Details
- Title
- Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)
- Creators
- Elizabeth Tseng - Pacific BiosciencesJason G Underwood - Pacific BiosciencesBrandon D Evans Hutzenbiler - School of the Environment, Washington State University, Pullman, WA 99164, USAShawn Trojahn - Washington State UniversityBrewster Kingham - Biotechnology InstituteOlga Shevchenko - Biotechnology InstituteErin Bernberg - Biotechnology InstituteMichelle Vierra - Pacific BiosciencesCharles T Robbins - Washington State University, Environment, School of the (CAHNRS)Heiko T Jansen - Washington State University, Integrative Physiology and Neuroscience, Department ofJoanna L Kelley - Washington State University, Biological Sciences, School of
- Publication Details
- G3 : genes - genomes - genetics, Vol.12(3)
- Academic Unit
- Kelley Lab
- Identifiers
- 99900882931701842
- Language
- English
- Resource Type
- Journal article