Two Ck1δ transcripts regulated by m6A methylation code for two antagonistic kinases in the control of the circadian clock

Regulation of N6-Methyladenosine in the Differentiation of Cancer Stem Cells and Their Fate

N6-methyladenosine (m6A) is one of the most common internal RNA modifications in eukaryotes. It is a dynamic and reversible process that requires an orchestrated participation of methyltransferase, demethylase, and methylated binding protein. m6A modification can affect RNA degradation, translation, and microRNA processing. m6A plays an important role in the regulation of various processes in living organisms. In addition to being involved in normal physiological processes such as sperm development, immunity, fat differentiation, cell development, and differentiation, it is also involved in tumor progression and stem cell differentiation. Curiously enough, cancer stem cells, a rare group of cells present in malignant tumors, retain the characteristics of stem cells and play an important role in the survival, proliferation, metastasis, and recurrence of cancers. Recently, studies demonstrated that m6A participates in the self-renewal and pluripotent regulation of these stem cells. However, considering that multiple targets of m6A are involved in different physiological processes, the exact role of m6A in cancer progression remains controversial. This article focuses on the mechanism of m6A and its effects on the differentiation of cancer stem cells, to provide a basis for elucidating the tumorigenesis mechanisms and exploring new potential therapeutic approaches.

New insights into non-transcriptional regulation of mammalian core clock proteins

Mammalian circadian rhythms drive ∼24 h periodicity in a wide range of cellular processes, temporally coordinating physiology and behaviour within an organism, and synchronising this with the external day-night cycle. The canonical model for this timekeeping consists of a delayed negative-feedback loop, containing transcriptional activator complex CLOCK-BMAL1 (BMAL1 is also known as ARNTL) and repressors period 1, 2 and 3 (PER1, PER2 and PER3) and cryptochrome 1 and 2 (CRY1 and CRY2), along with a number of accessory factors. Although the broad strokes of this system are defined, the exact molecular mechanisms by which these proteins generate a self-sustained rhythm with such periodicity and fidelity remains a topic of much research. Recent studies have identified prominent roles for a number of crucial post-transcriptional, translational and, particularly, post-translational events within the mammalian circadian oscillator, providing an increasingly complex understanding of the activities and interactions of the core clock proteins. In this Review, we highlight such contemporary work on non-transcriptional events and set it within our current understanding of cellular circadian timekeeping.

m6A RNA Methylation: Ramifications for Gene Expression and Human Health

Cellular transcriptomes are frequently adorned by a variety of chemical modification marks, which in turn have a profound influence on its functioning. Of these modifications, the one which has invited a lot of attention in the recent years is m6A RNA methylation, leading to the development of RNA epigenetics or epitranscriptomics as a frontier research area. m6A RNA methylation is one of the most abundant reversible internal modification seen in cellular RNAs. Studies in the last few years have not only shed light on the molecular machinery involved in m6A RNA methylation but also on the impact of this modification in regulating gene expression and hence biological processes. In this review, we will emphasize the biological impact of this modification in normal organismal development and diseases.

Coupled network of the circadian clocks: a driving force of rhythmic physiology

The circadian system is composed of coupled endogenous oscillators that allow living beings, including humans, to anticipate and adapt to daily changes in their environment. In mammals, circadian clocks form a hierarchically organized network with a 'master clock' located in the suprachiasmatic nucleus of the hypothalamus, which ensures entrainment of subsidiary oscillators to environmental cycles. Robust rhythmicity of body clocks is indispensable for temporally coordinating organ functions, and the disruption or misalignment of circadian rhythms caused for instance by modern lifestyle is strongly associated with various widespread diseases. This review aims to provide a comprehensive overview of our current knowledge about the molecular architecture and system-level organization of mammalian circadian oscillators. Furthermore, we discuss the regulatory roles of peripheral clocks for cell and organ physiology and their implication in the temporal coordination of metabolism in human health and disease. Finally, we summarize methods for assessing circadian rhythmicity in humans.

A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications

Cells use chemical modifications to alter the sterics, charge, and conformations of large biomolecules, modulating their biogenesis, function, and stability. Until recently post-transcriptional RNA modifications were thought to be largely limited to nonprotein coding RNA species. However, this dogma has rapidly transformed with the discovery of a host of modifications in protein coding messenger RNAs (mRNAs). Recent advancements in genome-wide sequencing technologies have enabled the identification of mRNA modifications as a potential new frontier in gene regulation-leading to the development of the epitranscriptome field. As a result, there has been a flurry of multiple groundbreaking discoveries, including new modifications, nucleoside modifying enzymes ("writers" and "erasers"), and RNA binding proteins that recognize chemical modifications ("readers"). These discoveries opened the door to understanding how post-transcriptional mRNA modifications can modulate the mRNA lifecycle, and established a link between the epitranscriptome and human health and disease. Despite a rapidly growing recognition of their importance, fundamental questions regarding the identity, prevalence, and functional consequences of mRNA modifications remain to be answered. Here, we highlight quantitative studies that characterize mRNA modification abundance, frequency, and interactions with cellular machinery. As the field progresses, we see a need for the further integration of quantitative and reductionist approaches to complement transcriptome wide studies in order to establish a molecular-level framework for understanding the consequences of mRNA chemical modifications on biological processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Processing > RNA Editing and Modification.

Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock

Mathematical models can enable a predictive understanding of mechanism in cell biology by quantitatively describing complex networks of interactions, but such models are often poorly constrained by available data. Owing to its relative biochemical simplicity, the core circadian oscillator in Synechococcus elongatus has become a prototypical system for studying how collective dynamics emerge from molecular interactions. The oscillator consists of only three proteins, KaiA, KaiB, and KaiC, and near-24-h cycles of KaiC phosphorylation can be reconstituted in vitro. Here, we formulate a molecularly detailed but mechanistically naive model of the KaiA-KaiC subsystem and fit it directly to experimental data within a Bayesian parameter estimation framework. Analysis of the fits consistently reveals an ultrasensitive response for KaiC phosphorylation as a function of KaiA concentration, which we confirm experimentally. This ultrasensitivity primarily results from the differential affinity of KaiA for competing nucleotide-bound states of KaiC. We argue that the ultrasensitive stimulus-response relation likely plays an important role in metabolic compensation by suppressing premature phosphorylation at nighttime.

Mutation of a PER2 phosphodegron perturbs the circadian phosphoswitch

The speed of the circadian clock is regulated by phosphorylation-regulated degradation of the PER protein. However, this model has recently been challenged by genetic studies in mice and fungi. Here, we provide definitive genetic and biochemical evidence that strongly supports the importance of the phosphoswitch-regulated proteolysis of PER2 in regulating the clock. We generated two independent mouse lines with a point mutation in a casein kinase 1-dependent phosphodegron in PER2. These mice have longer circadian rhythms, increased accumulation of circadian proteins, and perturbed temperature compensation. The findings strongly support the phosphoswitch model of regulated PER2 degradation as a central mechanism controlling the speed of the circadian clock.

Casein kinase 1 (CK1) plays a central role in regulating the period of the circadian clock. In mammals, PER2 protein abundance is regulated by CK1-mediated phosphorylation and proteasomal degradation. On the other hand, recent studies have questioned whether the degradation of the core circadian machinery is a critical step in clock regulation. Prior cell-based studies found that CK1 phosphorylation of PER2 at Ser478 recruits the ubiquitin E3 ligase β-TrCP, leading to PER2 degradation. Creation of this phosphodegron is regulated by a phosphoswitch that is also implicated in temperature compensation. However, in vivo evidence that this phosphodegron influences circadian period is lacking. Here, we generated and analyzed PER2-Ser478Ala knock-in mice. The mice showed longer circadian period in behavioral analysis. Molecularly, mutant PER2 protein accumulated in both the nucleus and cytoplasm of the mouse liver, while Per2 messenger RNA (mRNA) levels were minimally affected. Nuclear PER1, CRY1, and CRY2 proteins also increased, probably due to stabilization of PER2-containing complexes. In mouse embryonic fibroblasts derived from PER2-Ser478Ala::LUC mice, three-phase decay and temperature compensation of the circadian period was perturbed. These data provide direct in vivo evidence for the importance of phosphorylation-regulated PER2 stability in the circadian clock and validate the phosphoswitch in a mouse model.

Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch

Post-translational control of PERIOD stability by Casein Kinase 1δ and ε (CK1) plays a key regulatory role in metazoan circadian rhythms. Despite the deep evolutionary conservation of CK1 in eukaryotes, little is known about its regulation and the factors that influence substrate selectivity on functionally antagonistic sites in PERIOD that directly control circadian period. Here we describe a molecular switch involving a highly conserved anion binding site in CK1. This switch controls conformation of the kinase activation loop and determines which sites on mammalian PER2 are preferentially phosphorylated, thereby directly regulating PER2 stability. Integrated experimental and computational studies shed light on the allosteric linkage between two anion binding sites that dynamically regulate kinase activity. We show that period-altering kinase mutations from humans to Drosophila differentially modulate this activation loop switch to elicit predictable changes in PER2 stability, providing a foundation to understand and further manipulate CK1 regulation of circadian rhythms.

Methyltransferase like 3 promotes colorectal cancer proliferation by stabilizing CCNE1 mRNA in an m6A-dependent manner

m6A modification is the most prevalent RNA modification in eukaryotes. As the critical N6‐methyladenosine (m6A) methyltransferase, the roles of methyltransferase like 3 (METTL3) in colorectal cancer (CRC) are controversial. Here, we confirmed that METTL3, a critical m6A methyltransferase, could facilitate CRC progression in vitro and in vivo. Further, we found METTL3 promoted CRC cell proliferation by methylating the m6A site in 3′‐untranslated region (UTR) of CCNE1 mRNA to stabilize it. Moreover, we found butyrate, a classical intestinal microbial metabolite, could down‐regulate the expression of METTL3 and related cyclin E1 to inhibit CRC development. METTL3 promotes CRC proliferation by stabilizing CCNE1 mRNA in an m6A‐dependent manner, representing a promising therapeutic strategy for the treatment of CRC.

A five-gene signature derived from m6A regulators to improve prognosis prediction of neuroblastoma

BACKGROUND AND OBJECTIVE

N6-methyladenosine (m6a) is the most abundant form of methylated modification in eukaryotic mRNA. However, the role of m6A-related genes in neuroblastoma (NB), one of the most common paediatric malignant tumours, is not well known. This study aimed to determine the prognostic role of m6A-related genes in neuroblastoma.

METHODS

We analysed the expression of 20 published m6A methylation regulators in 498 patients with NB from the Gene Expression Omnibus database. To determine the independent prognostic factors, we used univariate Cox analysis, the least absolute shrinkage and selection operator (LASSO) regression. The multivariate Cox analysis was used to construct a prognostic risk prediction model. 120 NB tissues from "Therapeutically Applicable Research To Generate Effective Treatments" (TARGET ) database was used to test the prognostic value. Gene set enrichment analysis was performed to discover the potential biological function of the m6A signature.

RESULTS

The risk prediction model consisted of five genes (METT14, WTAP, HNRNPC, YTHDF1 and IGF2BP2). The receiving operating characteristic curve showed the high exactitude of the risk model. Cox regression analysis revealed that the risk model was an independent prognostic factor of overall survival. These results were reproduced using another published independent dataset. Further functional enrichment analysis suggested the involvement of the 5-gene signature in several malignancies.

CONCLUSION

The five m6A regulatory genes identified in this study enable clinical prognosis of NB and may serve as novel therapeutic targets for NB.

The importance of being rhythmic: Living in harmony with your body clocks

Circadian rhythms have developed in all light-sensitive organisms, including humans, as a fundamental anticipatory mechanism that enables proactive adaptation to environmental changes. The circadian system is organized in a highly hierarchical manner, with clocks operative in most cells of the body ensuring the temporal coordination of physiological processes. Circadian misalignment, stemming from modern life style, draws increasing attention due to its tight association with the development of metabolic, cardiovascular, inflammatory and mental diseases as well as cancer. This review highlights recent findings emphasizing the role of the circadian system in the temporal orchestration of physiology, with a particular focus on implications of circadian misalignment in human pathologies.

Theoretical study on the regulation of circadian rhythms by RNA methylation

Messenger RNAs are often destabilized by methylation, suggesting that mRNA methylation alters mRNA and protein dynamics. This may indicate that the gene regulatory system is reflected by the metabolic system through mRNA methylation because methylation substrates are components of the metabolic system. Elucidating the mechanisms by which mRNA methylation regulates gene regulatory systems has posed considerable challenges due to the numerous targets of mRNA methylation. Recent studies have demonstrated that inhibition of mRNA N6-methyladenosine methylation elongates circadian periods. The aim of this study was to understand the mechanisms by which mRNA methylation regulates circadian rhythms. Using a detailed realistic model and a simple model, we demonstrated that period elongation of circadian rhythms by decreasing mRNA methylation can be achieved by two possibilities, i.e., decreasing mRNA methylation stabilizes nonoscillatory mRNAs such as Ck1δ and/or stabilizes oscillatory mRNAs of clock genes such as Per and Cry. In addition, we predicted that period elongation by stabilizing nonoscillatory mRNA (Ck1δ) should always be accompanied by the distortion of the circadian waveform. Finally, we discuss the validity of the two possible mechanisms on the regulation of circadian rhythms by mRNA methylation by quantifying waveform distortion of circadian gene activity data with or without mRNA methylation inhibitors.

Rhythm on a chip: circadian entrainment in vitro is the next frontier in body-on-a chip technology

Organoids, bioprinted mini-tissues and body-on-a-chip technologies are poised to transform the practice of preclinical pharmacology, with a view to achieving better predictive value. We review the need for further refinement in static and dynamic biomechanical aspects of such microenvironments. Further consideration of the developments required in perfusion systems to enable delivery of an appropriate soluble microenvironment are argued. We place particular emphasis on a major deficiency in these systems, being the absence or aberrant circadian behaviour of cells used in such settings, and consider the technical challenges that are needing to be met in order to achieve rhythm-on-a-chip.

Structure, regulation, and (patho-)physiological functions of the stress-induced protein kinase CK1 delta (CSNK1D)

Members of the highly conserved pleiotropic CK1 family of serine/threonine-specific kinases are tightly regulated in the cell and play crucial regulatory roles in multiple cellular processes from protozoa to human. Since their dysregulation as well as mutations within their coding regions contribute to the development of various different pathologies, including cancer and neurodegenerative diseases, they have become interesting new drug targets within the last decade. However, to develop optimized CK1 isoform-specific therapeutics in personalized therapy concepts, a detailed knowledge of the regulation and functions of the different CK1 isoforms, their various splice variants and orthologs is mandatory. In this review we will focus on the stress-induced CK1 isoform delta (CK1δ), thereby addressing its regulation, physiological functions, the consequences of its deregulation for the development and progression of diseases, and its potential as therapeutic drug target.

Autokinase Activity of Casein Kinase 1 δ/ε Governs the Period of Mammalian Circadian Rhythms

Circadian rhythms exist in nearly all organisms. In mammals, transcriptional and translational feedback loops (TTFLs) are believed to underlie the mechanism of the circadian clock. Casein kinase 1δ/ε (CK1δ/ε) are key kinases that phosphorylate clock components such as PER proteins, determining the pace of the clock. Most previous studies of the biochemical properties of the key kinases CK1ε and CK1δ in vitro have focused on the properties of the catalytic domains from which the autoinhibitory C-terminus has been deleted (ΔC); those studies ignored the significance of self-inhibition by autophosphorylation. By comparing the properties of the catalytic domain of CK1δ/ε with the full-length kinase that can undergo autoinhibition, we found that recombinant full-length CK1 showed a sequential autophosphorylation process that induces conformational changes to affect the overall kinase activity. Furthermore, a direct relationship between the period change and the autokinase activity among CK1δ, CK1ε, and CK1ε-R178C was observed. These data implicate the autophosphorylation activity of CK1δ and CK1ε kinases in setting the pace of mammalian circadian rhythms and indicate that the circadian period can be modulated by tuning the autophosphorylation rates of CK1δ/ε.

N6-methyladenosine modifications: interactions with novel RNA-binding proteins and roles in signal transduction

RNA epigenetics has received a great deal of attention in recent years, and the reversible N6-methyladenosine (m6A) modification on messenger RNAs (mRNAs) has emerged as a widespread phenomenon. The vital roles of m6A in diverse biological processes are dependent on many RNA-binding proteins (RBPs) with 'reader' or 'nonreader' functions. Moreover, m6A effector proteins affect cellular processes, such as stem cell differentiation, tumor development and the immune response by controlling signal transduction. This review provides an overview of the interactions of m6A with various RBPs, including the 'reader' proteins (excluding the YT521-B homology (YTH) domain proteins and the heterogeneous nuclear ribonucleoproteins (hnRNPs)), and the functional 'nonreader' proteins, and this review focuses on their specific RNA-binding domains and their associations with other m6A effectors. Furthermore, we summarize key m6A-marked targets in distinct signaling pathways, leading to a better understanding of the cellular m6A machinery.

Reduced delivery of epididymal adipocyte-derived exosomal resistin is essential for melatonin ameliorating hepatic steatosis in mice

Adipocyte-derived exosomes (Exos) serve as bioinformation-containing messengers in cell-to-cell communications, and numerous reports demonstrate that resistin, an adipokine, is strongly associated with hepatic steatosis and other fatty liver diseases, suggesting that adipose dysfunction-generated altered pattern of exosomal cytokines may contribute to shaping the physiological activities in liver. Admittedly, melatonin-mediated positive effects on various tissues/organs have been respectively reported, but regulatory mechanisms of melatonin on the crosstalk between adipose tissue and liver have been investigated rarely. Overall, we hypothesize that the crosstalk originating from adipose tissue may be another worthy regulatory pathway for melatonin ameliorating of hepatic steatosis. Here, we first found the amount of adipocyte-derived exosomal resistin to be significantly decreased by melatonin supplementation. Compared to mice with Exos_HFD or Exos_resistin treatment, Exos_MT remarkably ameliorated hepatic steatosis. Further test demonstrated that resistin was a pivotal cytokine which repressed phosphorylation of 5' adenosine monophosphate-activated protein kinase α (pAMPKα Thr¹⁷² ) to trigger endoplasmic reticulum (ER) stress, resulting in hepatic steatosis, whereas Exos_MT reversed these risks in hepatocytes. In adipocytes, we identified melatonin to reduce the production of resistin through the brain and muscle arnt-like protein 1 (Bmal1) transcriptional inhibition. Notably, we also confirmed that melatonin enhanced N⁶ -Methyladenosine (m⁶ A) RNA demethylation to degrade resistin mRNA in adipocytes. Overall, melatonin decreases traffic volume of adipocyte-generated exosomal resistin from adipocytes to hepatocytes, which further alleviates ER stress-induced hepatic steatosis. Our findings illustrate a novel melatonin-mediated regulatory pathway from adipocytes to hepatocytes, indicating that adipocyte-derived exosome is a new potential target for treating obesity and related hepatorenal syndrome.

Non-sinusoidal Waveform in Temperature-Compensated Circadian Oscillations

Time series of biological rhythms are of various shapes. Here, we investigated the waveforms of circadian rhythms in gene-protein dynamics using a newly developed, to our knowledge, index to quantify the degree of distortion from a sinusoidal waveform. In general, most biochemical reactions accelerate with increasing temperature, but the period of circadian rhythms remains relatively stable with temperature change, a phenomenon known as "temperature compensation." Despite extensive research, the mechanism underlying this remains unclear. To understand the mechanism, we used transcriptional-translational oscillator models for circadian rhythms in the fruit fly Drosophila and mammals. Given the assumption that reaction rates increase with temperature, mathematical analyses revealed that temperature compensation required waveforms that are more nonsinusoidal at higher temperatures. We then analyzed a post-translational oscillator (PTO) model of cyanobacteria circadian rhythms. Because the structure of the PTO is different from that of the transcriptional-translational oscillator, the condition for temperature compensation would be expected to differ. Unexpectedly, the computational analysis again showed that temperature compensation in the PTO model required a more nonsinusoidal waveform at higher temperatures. This finding held for both models even with a milder assumption that some reaction rates do not change with temperature, which is consistent with experimental evidence. Together, our theoretical analyses predict that the waveform of circadian gene-activity and/or protein phosphorylation rhythms would be more nonsinusoidal at higher temperatures, even when there are differences in the network structures.

Periodicity, repression, and the molecular architecture of the mammalian circadian clock

Large molecular machines regulate daily cycles of transcriptional activity and help generate rhythmic behavior. In recent years, structural and biochemical analyses have elucidated a number of principles guiding the interactions of proteins that form the basis of circadian timing. In its simplest form, the circadian clock is composed of a transcription/translation feedback loop. However, this description elides a complicated process of activator recruitment, chromatin decompaction, recruitment of coactivators, expression of repressors, formation of a repressive complex, repression of the activators, and ultimately degradation of the repressors and reinitiation of the cycle. Understanding the core principles underlying the clock requires careful examination of molecular and even atomic level details of these processes. Here, we review major structural and biochemical findings in circadian biology and make the argument that shared protein interfaces within the clockwork are critical for both the generation of rhythmicity and timing of the clock.

CK1δ/ε protein kinase primes the PER2 circadian phosphoswitch

Our innate circadian clocks control myriad aspects of behavior and physiology. Disruption of our clocks by shift work, jet lag, or inherited mutation leads to metabolic dysregulation and contributes to diseases, including diabetes and cancer. A central step in clock control is phosphorylation of the PERIOD 2 (PER2) protein. Here we conclusively identify the elusive PER2 priming kinase and find it to be the well-known circadian kinase, casein kinase 1 (CK1). Surprisingly, different forms of CK1 have differing abilities to phosphorylate the PER2 priming site, adding to the complexity of circadian regulation. These insights into the phosphoregulation of PER2 will be of broad interest to circadian biologists, computational modelers, and those seeking to pharmacologically manipulate the circadian clock.

Multisite phosphorylation of the PERIOD 2 (PER2) protein is the key step that determines the period of the mammalian circadian clock. Previous studies concluded that an unidentified kinase is required to prime PER2 for subsequent phosphorylation by casein kinase 1 (CK1), an essential clock component that is conserved from algae to humans. These subsequent phosphorylations stabilize PER2, delay its degradation, and lengthen the period of the circadian clock. Here, we perform a comprehensive biochemical and biophysical analysis of mouse PER2 (mPER2) priming phosphorylation and demonstrate, surprisingly, that CK1δ/ε is indeed the priming kinase. We find that both CK1ε and a recently characterized CK1δ2 splice variant more efficiently prime mPER2 for downstream phosphorylation in cells than the well-studied splice variant CK1δ1. While CK1 phosphorylation of PER2 was previously shown to be robust to changes in the cellular environment, our phosphoswitch mathematical model of circadian rhythms shows that the CK1 carboxyl-terminal tail can allow the period of the clock to be sensitive to cellular signaling. These studies implicate the extreme carboxyl terminus of CK1 as a key regulator of circadian timing.