Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos)
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...
Published in: | G3 Genes|Genomes|Genetics |
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Language: | English |
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Oxford University Press (OUP)
2021
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Online Access: | http://dx.doi.org/10.1093/g3journal/jkab422 https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkab422/42350786/jkab422.pdf https://academic.oup.com/g3journal/article-pdf/12/3/jkab422/42731464/jkab422.pdf |
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croxfordunivpr:10.1093/g3journal/jkab422 2024-09-09T20:12:47+00:00 Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos) Tseng, Elizabeth Underwood, Jason G Evans Hutzenbiler, Brandon D Trojahn, Shawn Kingham, Brewster Shevchenko, Olga Bernberg, Erin Vierra, Michelle Robbins, Charles T Jansen, Heiko T Kelley, Joanna L Sethuraman, A Pacific Biosciences (PacBio) SMRT Interagency Grizzly Bear Committee, United States Department of Agriculture National Institute of Food and Agriculture International Association for Bear Research and Management T. N. Tollefson and Mazuri Exotic Animal Nutrition Raili Korkka Brown Bear Endowment Nutritional Ecology Endowment, and Bear Research and Conservation Endowment 2021 http://dx.doi.org/10.1093/g3journal/jkab422 https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkab422/42350786/jkab422.pdf https://academic.oup.com/g3journal/article-pdf/12/3/jkab422/42731464/jkab422.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by/4.0/ G3 Genes|Genomes|Genetics volume 12, issue 3 ISSN 2160-1836 journal-article 2021 croxfordunivpr https://doi.org/10.1093/g3journal/jkab422 2024-08-12T04:25:02Z 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. Article in Journal/Newspaper Ursus arctos Oxford University Press G3 Genes|Genomes|Genetics |
institution |
Open Polar |
collection |
Oxford University Press |
op_collection_id |
croxfordunivpr |
language |
English |
description |
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. |
author2 |
Sethuraman, A Pacific Biosciences (PacBio) SMRT Interagency Grizzly Bear Committee, United States Department of Agriculture National Institute of Food and Agriculture International Association for Bear Research and Management T. N. Tollefson and Mazuri Exotic Animal Nutrition Raili Korkka Brown Bear Endowment Nutritional Ecology Endowment, and Bear Research and Conservation Endowment |
format |
Article in Journal/Newspaper |
author |
Tseng, Elizabeth Underwood, Jason G Evans Hutzenbiler, Brandon D Trojahn, Shawn Kingham, Brewster Shevchenko, Olga Bernberg, Erin Vierra, Michelle Robbins, Charles T Jansen, Heiko T Kelley, Joanna L |
spellingShingle |
Tseng, Elizabeth Underwood, Jason G Evans Hutzenbiler, Brandon D Trojahn, Shawn Kingham, Brewster Shevchenko, Olga Bernberg, Erin Vierra, Michelle Robbins, Charles T Jansen, Heiko T Kelley, Joanna L Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos) |
author_facet |
Tseng, Elizabeth Underwood, Jason G Evans Hutzenbiler, Brandon D Trojahn, Shawn Kingham, Brewster Shevchenko, Olga Bernberg, Erin Vierra, Michelle Robbins, Charles T Jansen, Heiko T Kelley, Joanna L |
author_sort |
Tseng, Elizabeth |
title |
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos) |
title_short |
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos) |
title_full |
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos) |
title_fullStr |
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos) |
title_full_unstemmed |
Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( Ursus arctos) |
title_sort |
long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears ( ursus arctos) |
publisher |
Oxford University Press (OUP) |
publishDate |
2021 |
url |
http://dx.doi.org/10.1093/g3journal/jkab422 https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkab422/42350786/jkab422.pdf https://academic.oup.com/g3journal/article-pdf/12/3/jkab422/42731464/jkab422.pdf |
genre |
Ursus arctos |
genre_facet |
Ursus arctos |
op_source |
G3 Genes|Genomes|Genetics volume 12, issue 3 ISSN 2160-1836 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1093/g3journal/jkab422 |
container_title |
G3 Genes|Genomes|Genetics |
_version_ |
1809947403505106944 |