Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal

Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Rui Fu [verfasserIn] Austin E. Gillen [verfasserIn] Katharine R. Grabek [verfasserIn] Kent A. Riemondy [verfasserIn] L. Elaine Epperson [verfasserIn] Carlos D. Bustamante [verfasserIn] Jay R. Hesselberth [verfasserIn] Sandra L. Martin [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	AU-rich element (ARE) ARE binding proteins forebrain hypothalamus Ictidomys tridecemlineatus medulla

Übergeordnetes Werk:	In: Frontiers in Physiology - Frontiers Media S.A., 2011, 11(2021)
Übergeordnetes Werk:	volume:11 ; year:2021

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fphys.2020.624677

Katalog-ID:	DOAJ051004364

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allfields	10.3389/fphys.2020.624677 doi (DE-627)DOAJ051004364 (DE-599)DOAJ462c20f488da4952b8b758bfab9f3520 DE-627 ger DE-627 rakwb eng QP1-981 Rui Fu verfasserin aut Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health. AU-rich element (ARE) ARE binding proteins forebrain hypothalamus Ictidomys tridecemlineatus medulla Physiology Austin E. Gillen verfasserin aut Katharine R. Grabek verfasserin aut Katharine R. Grabek verfasserin aut Kent A. Riemondy verfasserin aut L. Elaine Epperson verfasserin aut Carlos D. Bustamante verfasserin aut Jay R. Hesselberth verfasserin aut Jay R. Hesselberth verfasserin aut Sandra L. Martin verfasserin aut Sandra L. Martin verfasserin aut In Frontiers in Physiology Frontiers Media S.A., 2011 11(2021) (DE-627)631498788 (DE-600)2564217-0 1664042X nnns volume:11 year:2021 https://doi.org/10.3389/fphys.2020.624677 kostenfrei https://doaj.org/article/462c20f488da4952b8b758bfab9f3520 kostenfrei https://www.frontiersin.org/articles/10.3389/fphys.2020.624677/full kostenfrei https://doaj.org/toc/1664-042X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021
spelling	10.3389/fphys.2020.624677 doi (DE-627)DOAJ051004364 (DE-599)DOAJ462c20f488da4952b8b758bfab9f3520 DE-627 ger DE-627 rakwb eng QP1-981 Rui Fu verfasserin aut Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health. AU-rich element (ARE) ARE binding proteins forebrain hypothalamus Ictidomys tridecemlineatus medulla Physiology Austin E. Gillen verfasserin aut Katharine R. Grabek verfasserin aut Katharine R. Grabek verfasserin aut Kent A. Riemondy verfasserin aut L. Elaine Epperson verfasserin aut Carlos D. Bustamante verfasserin aut Jay R. Hesselberth verfasserin aut Jay R. Hesselberth verfasserin aut Sandra L. Martin verfasserin aut Sandra L. Martin verfasserin aut In Frontiers in Physiology Frontiers Media S.A., 2011 11(2021) (DE-627)631498788 (DE-600)2564217-0 1664042X nnns volume:11 year:2021 https://doi.org/10.3389/fphys.2020.624677 kostenfrei https://doaj.org/article/462c20f488da4952b8b758bfab9f3520 kostenfrei https://www.frontiersin.org/articles/10.3389/fphys.2020.624677/full kostenfrei https://doaj.org/toc/1664-042X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021
allfields_unstemmed	10.3389/fphys.2020.624677 doi (DE-627)DOAJ051004364 (DE-599)DOAJ462c20f488da4952b8b758bfab9f3520 DE-627 ger DE-627 rakwb eng QP1-981 Rui Fu verfasserin aut Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health. AU-rich element (ARE) ARE binding proteins forebrain hypothalamus Ictidomys tridecemlineatus medulla Physiology Austin E. Gillen verfasserin aut Katharine R. Grabek verfasserin aut Katharine R. Grabek verfasserin aut Kent A. Riemondy verfasserin aut L. Elaine Epperson verfasserin aut Carlos D. Bustamante verfasserin aut Jay R. Hesselberth verfasserin aut Jay R. Hesselberth verfasserin aut Sandra L. Martin verfasserin aut Sandra L. Martin verfasserin aut In Frontiers in Physiology Frontiers Media S.A., 2011 11(2021) (DE-627)631498788 (DE-600)2564217-0 1664042X nnns volume:11 year:2021 https://doi.org/10.3389/fphys.2020.624677 kostenfrei https://doaj.org/article/462c20f488da4952b8b758bfab9f3520 kostenfrei https://www.frontiersin.org/articles/10.3389/fphys.2020.624677/full kostenfrei https://doaj.org/toc/1664-042X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021
allfieldsGer	10.3389/fphys.2020.624677 doi (DE-627)DOAJ051004364 (DE-599)DOAJ462c20f488da4952b8b758bfab9f3520 DE-627 ger DE-627 rakwb eng QP1-981 Rui Fu verfasserin aut Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health. AU-rich element (ARE) ARE binding proteins forebrain hypothalamus Ictidomys tridecemlineatus medulla Physiology Austin E. Gillen verfasserin aut Katharine R. Grabek verfasserin aut Katharine R. Grabek verfasserin aut Kent A. Riemondy verfasserin aut L. Elaine Epperson verfasserin aut Carlos D. Bustamante verfasserin aut Jay R. Hesselberth verfasserin aut Jay R. Hesselberth verfasserin aut Sandra L. Martin verfasserin aut Sandra L. Martin verfasserin aut In Frontiers in Physiology Frontiers Media S.A., 2011 11(2021) (DE-627)631498788 (DE-600)2564217-0 1664042X nnns volume:11 year:2021 https://doi.org/10.3389/fphys.2020.624677 kostenfrei https://doaj.org/article/462c20f488da4952b8b758bfab9f3520 kostenfrei https://www.frontiersin.org/articles/10.3389/fphys.2020.624677/full kostenfrei https://doaj.org/toc/1664-042X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2021
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topic_title	QP1-981 Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal AU-rich element (ARE) ARE binding proteins forebrain hypothalamus Ictidomys tridecemlineatus medulla
topic	misc QP1-981 misc AU-rich element (ARE) misc ARE binding proteins misc forebrain misc hypothalamus misc Ictidomys tridecemlineatus misc medulla misc Physiology
topic_unstemmed	misc QP1-981 misc AU-rich element (ARE) misc ARE binding proteins misc forebrain misc hypothalamus misc Ictidomys tridecemlineatus misc medulla misc Physiology
topic_browse	misc QP1-981 misc AU-rich element (ARE) misc ARE binding proteins misc forebrain misc hypothalamus misc Ictidomys tridecemlineatus misc medulla misc Physiology
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title	Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
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title_full	Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
author_sort	Rui Fu
journal	Frontiers in Physiology
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author_browse	Rui Fu Austin E. Gillen Katharine R. Grabek Kent A. Riemondy L. Elaine Epperson Carlos D. Bustamante Jay R. Hesselberth Sandra L. Martin
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title_sort	dynamic rna regulation in the brain underlies physiological plasticity in a hibernating mammal
callnumber	QP1-981
title_auth	Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
abstract	Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health.
abstractGer	Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health.
abstract_unstemmed	Hibernation is a physiological and behavioral phenotype that minimizes energy expenditure. Hibernators cycle between profound depression and rapid hyperactivation of multiple physiological processes, challenging our concept of mammalian homeostasis. How the hibernator orchestrates and survives these extremes while maintaining cell to organismal viability is unknown. Here, we enhance the genome integrity and annotation of a model hibernator, the 13-lined ground squirrel. Our new assembly brings this genome to near chromosome-level contiguity and adds thousands of previously unannotated genes. These new genomic resources were used to identify 6,505 hibernation-related, differentially-expressed and processed transcripts using RNA-seq data from three brain regions in animals whose physiological status was precisely defined using body temperature telemetry. A software tool, squirrelBox, was developed to foster further data analyses and visualization. SquirrelBox includes a comprehensive toolset for rapid visualization of gene level and cluster group dynamics, sequence scanning of k-mer and domains, and interactive exploration of gene lists. Using these new tools and data, we deconvolute seasonal from temperature-dependent effects on the brain transcriptome during hibernation for the first time, highlighting the importance of carefully timed samples for studies of differential gene expression in hibernation. The identified genes include a regulatory network of RNA binding proteins that are dynamic in hibernation along with the composition of the RNA pool. In addition to passive effects of temperature, we provide evidence for regulated transcription and RNA turnover during hibernation. Significant alternative splicing, largely temperature dependent, also occurs during hibernation. These findings form a crucial first step and provide a roadmap for future work toward defining novel mechanisms of tissue protection and metabolic depression that may 1 day be applied toward improving human health.
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title_short	Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
url	https://doi.org/10.3389/fphys.2020.624677 https://doaj.org/article/462c20f488da4952b8b758bfab9f3520 https://www.frontiersin.org/articles/10.3389/fphys.2020.624677/full https://doaj.org/toc/1664-042X
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author2	Austin E. Gillen Katharine R. Grabek Kent A. Riemondy L. Elaine Epperson Carlos D. Bustamante Jay R. Hesselberth Sandra L. Martin
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