Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network

In recent years, it has become increasingly apparent that antisense transcription plays an important role in the regulation of gene expression. The circadian clock is no exception: an antisense transcript of the mammalian core-clock gene PERIOD2 (PER2), which we shall refer to as Per2AS RNA, oscillates with a circadian period and a nearly 12 h phase shift from the peak expression of Per2 mRNA. In this paper, we ask whether Per2AS plays a regulatory role in the mammalian circadian clock by studying in silico the potential effects of interactions between Per2 and Per2AS RNAs on circadian rhythms. Based on the antiphasic expression pattern, we consider two hypotheses about how Per2 and Per2AS mutually interfere with each other's expression. In our pre-transcriptional model, the transcription of Per2AS RNA from the non-coding strand represses the transcription of Per2 mRNA from the coding strand and vice versa. In our post-transcriptional model, Per2 and Per2AS transcripts form a double-stranded RNA duplex, which is rapidly degraded. To study these two possible mechanisms, we have added terms describing our alternative hypotheses to a published mathematical model of the molecular regulatory network of the mammalian circadian clock. Our pre-transcriptional model predicts that transcriptional interference between Per2 and Per2AS can generate alternative modes of circadian oscillations, which we characterize in terms of the amplitude and phase of oscillation of core clock genes. In our post-transcriptional model, Per2/Per2AS duplex formation dampens the circadian rhythm. In a model that combines pre- and post-transcriptional controls, the period, amplitude and phase of circadian proteins exhibit non-monotonic dependencies on the rate of expression of Per2AS. All three models provide potential explanations of the observed antiphasic, circadian oscillations of Per2 and Per2AS RNAs. They make discordant predictions that can be tested experimentally in order to distinguish among these alternative hypotheses.Author summary: A better understanding of the molecular mechanisms underlying circadian rhythms will undoubtedly improve the treatment of human health problems related to circadian dysrhythmias. However, the inventory of genes and genetic interactions in the circadian clock is still incomplete. Important players may yet be unknown or under-appreciated. For example, in mouse liver, the core clock gene PER2 is transcribed into both a Per2 mRNA molecule (a ‘sense’ transcript) and an antisense RNA transcript (Per2AS). Because it is important to know how interactions between Per2 and Per2AS may affect circadian gene expression, we have carried out a mathematical modeling study of two possible mechanisms for these interactions. In the pre-transcriptional model, Per2 mRNA interferes with the transcription of Per2AS RNA and vice versa. In the post-transcriptional model, Per2 and Per2AS molecules form double-stranded RNA duplexes, which are rapidly degraded by RNases. We find that the pre-transcriptional model gives a more robust account of the circadian, antiphasic oscillations of Per2 and Per2AS transcripts in mouse liver. The model makes an unexpected prediction that co-overexpression of the ROR gene and Per2AS sequences can generate a new mode of circadian oscillations not seen in contemporary models of circadian rhythms and not yet looked for experimentally.