Data_Sheet_1_Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal.pdf

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.

冬眠（Hibernation）是一种可最大限度减少能量消耗的生理与行为表型。冬眠动物（Hibernator）会在多重生理过程的深度抑制与快速过度激活之间循环往复，这对我们已有的哺乳动物内稳态（homeostasis）认知构成了挑战。目前学界尚未明确冬眠动物是如何协调并耐受这些极端生理状态，同时维持从细胞到个体全层级的生存活力的。本研究对模式冬眠动物——13线地松鼠（13-lined ground squirrel）的基因组完整性与注释信息进行了优化完善。新组装的基因组已达到近乎染色体级别的连续性，并新增了数千个此前未被注释的基因。研究人员借助通过体温遥测技术精准界定生理状态的动物的三个脑区的RNA测序（RNA-seq）数据，结合这些全新的基因组资源，共鉴定出6505个与冬眠相关的差异表达与加工转录本。为推动后续数据分析与可视化研究，本研究开发了一款名为squirrelBox的软件工具。该工具整合了一套全面的工具集，可实现基因表达水平与聚类群动态的快速可视化、k-mer与结构域的序列扫描，以及基因列表的交互式探索。借助这些全新的工具与数据，本研究首次实现了冬眠过程中大脑转录组所受季节效应与温度依赖效应的解卷积分析，凸显了精准定时采样对于冬眠差异基因表达研究的重要性。鉴定得到的基因包含一类在冬眠过程中动态变化的RNA结合蛋白调控网络，以及RNA池（RNA pool）的组成变化特征。除温度带来的被动影响外，本研究还为冬眠过程中受调控的转录与RNA周转（RNA turnover）提供了证据支持。冬眠过程中还存在大量可变剪接事件，且此类事件大多受温度调控。本研究的发现是阐明新型组织保护与代谢抑制机制的关键第一步，同时为后续相关研究提供了清晰蓝图——此类机制未来或可应用于改善人类健康。