Post-Transcriptional Circadian Regulation in Macrophages Organizes Temporally Distinct Immunometabolic States

Abstract

Our core timekeeping mechanism, the circadian clock, regulates an astonishing amount of cellular physiology and behavior, playing a vital role in organismal fitness. While the mechanics of circadian control over cellular regulation can in part be explained by the transcriptional activation stemming from the positive arm of the clock's transcription-translation negative feedback loop, research has shown that extensive circadian regulation occurs beyond transcriptional activation in fungal species and data suggest that this post-transcriptional regulation may also be preserved in mammals. To determine the extent to which circadian output is regulated post-transcriptionally in mammalian cells, we comprehensively profiled the transcriptome and proteome of murine bone marrow-derived macrophages in a high resolution, sample rich time course. We found that only 15% of the circadian proteome had corresponding oscillating mRNA and this regulation was cell intrinsic. Ontological analysis of oscillating proteins revealed robust temporal enrichment for protein degradation and translation, providing potential insights into the source of this extensive posttranscriptional regulation. We noted post-transcriptional temporal-gating across a number of connected metabolic pathways. This temporal metabolic regulation further corresponded with rhythms we observed in ATP production, mitochondrial morphology, and phagocytosis. With the strong interconnection between cellular metabolic states and macrophage phenotypes/responses, our work demonstrates that post-transcriptional circadian regulation in macrophages is broadly utilized as a tool to confer time-dependent immune function and responses. As macrophages coordinate many immunological and inflammatory functions, an understanding of this regulation provides a framework to determine the impact of circadian regulation on a wide array of disease pathologies.

Intrinsic disorder is an essential characteristic of components in the conserved circadian circuit

“…The rhythmic transcriptional activation on the promoters of these genes from the positive arm is believed to be the primary mechanism of output. In addition, recent work in several eukaryotic species has also shown that there is a great deal of post-transcriptional regulation, for example rhythmic proteins arising from non-rhythmic transcripts [22,[41][42][43][44][45]. This suggests that the canonical TTFL control of output has several as yet undiscovered levels of regulation.…”

Circadian rhythms in septic shock patients

“…Immune cell function is dependent on a 24-h circadian rhythm that is regulated by the expression of clock genes [ 10 , 11 ]. Key immune cell types, macrophages and monocytes, have a robust intrinsic circadian clock and a high expression of clock genes [ 12 ]. Molecular circadian rhythms are generated by autoregulatory transcription–translation feedback loops [ 13 ].…”

MOSAIC: a joint modeling methodology for combined circadian and non-circadian analysis of multi-omics data

“…the cell cycle. As multi-omics circadian data becomes more prevalent (Collins et al, 2020;Campbell et al, 2020;Hughes et al, 2017), MOSAIC will provide an important role in finding and understanding both oscillatory and non-oscillatory trends in a variety of organisms and processes.…”

“…Hurley et al (2018), that rhythmic RNA expression does not necessarily imply rhythmic protein expression and vice versa (Hurley et al, 2018), These data suggest that there may be extensive post-transcriptional regulation in the clock's output and beyond. The exact mechanisms of this regulation are currently unknown, though translation and degradation are predicted to be involved (Hurley et al, 2018;Lück et al, 2014;Collins et al, 2020).…”