During winter, hibernators are able to conserve energy during times of limited resources through the virtual cessation of energetically expensive processes that are thought to be intrinsic to the cell in homeostasis. During prolonged hibernation, these mammals, such as the 13-lined ground squirrel (Ictidomys tridecemlineatus), shut down the bulk of transcription and translation in order to preserve resources yet still require the expression of subsets of genes to assist with the challenges encountered during hibernation. Hibernators provide a unique opportunity for examining the dynamics of circadian clock activation in a system that requires the selection of groups of transcripts against a backdrop of suppressed cellular activity. This research shows that peripheral circadian clocks are regulated and have adapted to function in a tissue-specific manner that is congruent with the tissues functions during hibernation. In addition, substantial transcriptional and post-transcriptional machineries are required to endure deep torpor and low body temperature, including increased regulation over genomic activity by epigenetic enzymes. Both RNA adenosine and protein arginine methylation act to regulate activity within the circadian clock via epigenetic mechanisms and provide novel opportunities to uncover information about the post-translational modifications used during hibernation. RNA N6-methyladenosine (m6A) dynamics were maintained during hibernation and levels of m6A were increased on mRNA transcripts during torpor in liver. Responses by protein arginine methyltransferase (PRMT) enzymes were tissue-specific and within liver and white adipose, revealed responses that characterized metabolic reprogramming, whereas skeletal muscle PRMT activity was centered around transcriptional regulation. This research suggests that dynamic epigenetic modifications provide a mechanism for maintaining translation of selected groups of necessary transcripts during hibernation, including core circadian clock genes, against a backdrop of stunted transcript processing. These data also provide evidence that the circadian clock is an important and integral regulator of peripheral tissues within the mammalian hibernation phenotype.