Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos )
Abstract Hibernation in brown bears is an annual process involving multiple physiologically distinct seasons—hibernation, active, and hyperphagia. While recent studies have characterized broad patterns of differential gene regulation and isoform usage between hibernation and active seasons, patterns...
Published in: | Integrative and Comparative Biology |
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Oxford University Press (OUP)
2022
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Online Access: | http://dx.doi.org/10.1093/icb/icac093 https://academic.oup.com/icb/advance-article-pdf/doi/10.1093/icb/icac093/44784796/icac093.pdf https://academic.oup.com/icb/article-pdf/62/6/1802/48448169/icac093.pdf |
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croxfordunivpr:10.1093/icb/icac093 2023-12-31T10:23:53+01:00 Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos ) Perry, Blair W Armstrong, Ellie E Robbins, Charles T Jansen, Heiko T Kelley, Joanna L National Science Foundation United States Department of Agriculture National Institute of Food and Agriculture Washington Research Foundation 2022 http://dx.doi.org/10.1093/icb/icac093 https://academic.oup.com/icb/advance-article-pdf/doi/10.1093/icb/icac093/44784796/icac093.pdf https://academic.oup.com/icb/article-pdf/62/6/1802/48448169/icac093.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model Integrative And Comparative Biology volume 62, issue 6, page 1802-1811 ISSN 1540-7063 1557-7023 Plant Science Animal Science and Zoology journal-article 2022 croxfordunivpr https://doi.org/10.1093/icb/icac093 2023-12-06T08:42:42Z Abstract Hibernation in brown bears is an annual process involving multiple physiologically distinct seasons—hibernation, active, and hyperphagia. While recent studies have characterized broad patterns of differential gene regulation and isoform usage between hibernation and active seasons, patterns of gene and isoform expression during hyperphagia remain relatively poorly understood. The hyperphagia stage occurs between active and hibernation seasons and involves the accumulation of large fat reserves in preparation for hibernation. Here, we use time-series analyses of gene expression and isoform usage to interrogate transcriptomic regulation associated with all three seasons. We identify a large number of genes with significant differential isoform usage (DIU) across seasons and show that these patterns of isoform usage are largely tissue-specific. We also show that DIU and differential gene-level expression responses are generally non-overlapping, with only a small subset of multi-isoform genes showing evidence of both gene-level expression changes and changes in isoform usage across seasons. Additionally, we investigate nuanced regulation of candidate genes involved in the insulin signaling pathway and find evidence of hyperphagia-specific gene expression and isoform regulation that may enhance fat accumulation during hyperphagia. Our findings highlight the value of using temporal analyses of both gene- and isoform-level gene expression when interrogating complex physiological phenotypes and provide new insight into the mechanisms underlying seasonal changes in bear physiology. Article in Journal/Newspaper Ursus arctos Oxford University Press (via Crossref) Integrative and Comparative Biology |
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Oxford University Press (via Crossref) |
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croxfordunivpr |
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English |
topic |
Plant Science Animal Science and Zoology |
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Plant Science Animal Science and Zoology Perry, Blair W Armstrong, Ellie E Robbins, Charles T Jansen, Heiko T Kelley, Joanna L Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos ) |
topic_facet |
Plant Science Animal Science and Zoology |
description |
Abstract Hibernation in brown bears is an annual process involving multiple physiologically distinct seasons—hibernation, active, and hyperphagia. While recent studies have characterized broad patterns of differential gene regulation and isoform usage between hibernation and active seasons, patterns of gene and isoform expression during hyperphagia remain relatively poorly understood. The hyperphagia stage occurs between active and hibernation seasons and involves the accumulation of large fat reserves in preparation for hibernation. Here, we use time-series analyses of gene expression and isoform usage to interrogate transcriptomic regulation associated with all three seasons. We identify a large number of genes with significant differential isoform usage (DIU) across seasons and show that these patterns of isoform usage are largely tissue-specific. We also show that DIU and differential gene-level expression responses are generally non-overlapping, with only a small subset of multi-isoform genes showing evidence of both gene-level expression changes and changes in isoform usage across seasons. Additionally, we investigate nuanced regulation of candidate genes involved in the insulin signaling pathway and find evidence of hyperphagia-specific gene expression and isoform regulation that may enhance fat accumulation during hyperphagia. Our findings highlight the value of using temporal analyses of both gene- and isoform-level gene expression when interrogating complex physiological phenotypes and provide new insight into the mechanisms underlying seasonal changes in bear physiology. |
author2 |
National Science Foundation United States Department of Agriculture National Institute of Food and Agriculture Washington Research Foundation |
format |
Article in Journal/Newspaper |
author |
Perry, Blair W Armstrong, Ellie E Robbins, Charles T Jansen, Heiko T Kelley, Joanna L |
author_facet |
Perry, Blair W Armstrong, Ellie E Robbins, Charles T Jansen, Heiko T Kelley, Joanna L |
author_sort |
Perry, Blair W |
title |
Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos ) |
title_short |
Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos ) |
title_full |
Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos ) |
title_fullStr |
Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos ) |
title_full_unstemmed |
Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears ( Ursus arctos ) |
title_sort |
temporal analysis of gene expression and isoform switching in brown bears ( ursus arctos ) |
publisher |
Oxford University Press (OUP) |
publishDate |
2022 |
url |
http://dx.doi.org/10.1093/icb/icac093 https://academic.oup.com/icb/advance-article-pdf/doi/10.1093/icb/icac093/44784796/icac093.pdf https://academic.oup.com/icb/article-pdf/62/6/1802/48448169/icac093.pdf |
genre |
Ursus arctos |
genre_facet |
Ursus arctos |
op_source |
Integrative And Comparative Biology volume 62, issue 6, page 1802-1811 ISSN 1540-7063 1557-7023 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1093/icb/icac093 |
container_title |
Integrative and Comparative Biology |
_version_ |
1786835691614765056 |