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

Rui Fu,Carlos D Bustamante,Jay R Hesselberth,Austin E Gillen,Katharine R Grabek,L Elaine Epperson,Kent A Riemondy,Sandra L Martin

doi:10.3389/fphys.2020.624677

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.

Highlights

Hibernating mammals exhibit extreme and highly predictable physiological plasticity across daily, seasonal and annual cycles
While a full understanding of hibernation will require defining differential expression in tissues throughout the body, here we focus on three brain regions: forebrain, hypothalamus and medulla
We hypothesized that genes involved in tissue protection and metabolic suppression during hibernation are differentially expressed by timing in the seasonal or body temperature cycle, respectively, and would be revealed by the relative abundance of their transcripts in our sample groups

Summary

Introduction

Hibernating mammals exhibit extreme and highly predictable physiological plasticity across daily, seasonal and annual cycles. Most impressively, they temporarily suspend the mammalian trait of homeothermy by suppressing metabolic heat production. They temporarily suspend the mammalian trait of homeothermy by suppressing metabolic heat production This block allows body temperature (Tb) to drop to near freezing, and the animal to enter a state of deep torpor. By spending much of their fall and winter months in torpor, hibernators achieve profound energetic savings compared to what would be required to maintain Tb at 37◦C when environmental temperatures are near or below freezing (reviewed in Staples, 2016). Ictidomys tridecemlineatus (13-lined ground squirrels) alternate between a spring and summer active period of reproduction, growth and fattening, and the fall and winter hibernation period (Carey et al, 2003)

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