Table_5_Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability.XLSX

Hibernators dramatically lower metabolism to save energy while fasting for months. Prolonged fasting challenges metabolic homeostasis, yet small-bodied hibernators emerge each spring ready to resume all aspects of active life, including immediate reproduction. The liver is the body’s metabolic hub, processing and detoxifying macromolecules to provide essential fuels to brain, muscle and other organs throughout the body. Here we quantify changes in liver gene expression across several distinct physiological states of hibernation in 13-lined ground squirrels, using RNA-seq to measure the steady-state transcriptome and GRO-seq to measure transcription for the first time in a hibernator. Our data capture key timepoints in both the seasonal and torpor-arousal cycles of hibernation. Strong positive correlation between transcription and the transcriptome indicates that transcriptional control dominates the known seasonal reprogramming of metabolic gene expression in liver for hibernation. During the torpor-arousal cycle, however, discordance develops between transcription and the steady-state transcriptome by at least two mechanisms: 1) although not transcribed during torpor, some transcripts are unusually stable across the torpor bout; and 2) unexpectedly, on some genes, our data suggest continuing, slow elongation with a failure to terminate transcription across the torpor bout. While the steady-state RNAs corresponding to these read through transcripts did not increase during torpor, they did increase shortly after rewarming despite their simultaneously low transcription. Both of these mechanisms would assure the immediate availability of functional transcripts upon rewarming. Integration of transcriptional, post-transcriptional and RNA stability control mechanisms, all demonstrated in these data, likely initiate a serial gene expression program across the short euthermic period that restores the tissue and prepares the animal for the next bout of torpor.冬眠动物在长达数月的禁食期间，会显著降低新陈代谢水平以节约能量。长期禁食会对机体代谢稳态构成严峻挑战，但体型小巧的冬眠动物每年春季苏醒后，即可迅速恢复活跃生命的全部活动，包括即刻开展繁殖行为。肝脏是机体的代谢枢纽，可对大分子物质进行加工与解毒，为大脑、肌肉及全身其他器官提供必需的能量底物。本研究以十三线地松鼠（13-lined ground squirrels）为实验对象，针对冬眠过程中多个不同生理状态下的肝脏基因表达变化进行定量分析：首次在冬眠动物中采用RNA测序（RNA-seq）检测稳态转录组，并使用全局运行转录测序（GRO-seq）测定转录活性。我们的数据集覆盖了冬眠季节性周期与蛰伏-觉醒循环中的关键时间节点。转录活性与稳态转录组之间存在显著正相关关系，表明转录调控主导了已知的冬眠肝脏代谢基因表达季节性重编程过程。然而在蛰伏-觉醒循环中，转录活性与稳态转录组之间出现了至少两种机制介导的表达失调：其一，部分转录本在蛰伏期不发生转录，但在整个蛰伏过程中保持异常稳定的丰度；其二，令人意外的是，部分基因的转录组数据显示，在整个蛰伏周期内，RNA聚合酶仍在持续缓慢延伸，但无法正常终止转录。尽管此类通读转录本对应的稳态RNA在蛰伏期未出现丰度上升，但在复温后短时间内其丰度显著升高，尽管此时其转录活性仍处于较低水平。上述两种机制均可确保复温后功能性转录本可即刻发挥生物学功能。本研究数据证实了转录调控、转录后调控与RNA稳定性调控等多种机制的协同作用：这些机制可能在短暂的常态体温期内启动一系列连贯的基因表达程序，以修复肝脏组织，并为下一次蛰伏做好准备。