Circadian systems biology in Metazoa

Systems biology, which can be defined as integrative biology, comprises multistage processes that can be used to understand components of complex biological systems of living organisms and provides hierarchical information to decoding life. Using systems biology approaches such as genomics, transcriptomics and proteomics, it is now possible to delineate more complicated interactions between circadian control systems and diseases. The circadian rhythm is a multiscale phenomenon existing within the body that influences numerous physiological activities such as changes in gene expression, protein turnover, metabolism and human behavior. In this review, we describe the relationships between the circadian control system and its related genes or proteins, and circadian rhythm disorders in systems biology studies. To maintain and modulate circadian oscillation, cells possess elaborative feedback loops composed of circadian core proteins that regulate the expression of other genes through their transcriptional activities. The disruption of these rhythms has been reported to be associated with diseases such as arrhythmia, obesity, insulin resistance, carcinogenesis and disruptions in natural oscillations in the control of cell growth. This review demonstrates that lifestyle is considered as a fundamental factor that modifies circadian rhythm, and the development of dysfunctions and diseases could be regulated by an underlying expression network with multiple circadian-associated signals.

• Publication year

  2015

• Venue

  Briefings Bioinform.

• Publication date

  2015-03-10

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bib/bbv006PMID 25758249
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Mistimed sleep disrupts circadian regulation of the human transcriptome

  2014cited by this paper
• Induction of the CLOCK Gene by E2-ERα Signaling Promotes the Proliferation of Breast Cancer Cells

  2014cited by this paper
• REV-ERB and ROR nuclear receptors as drug targets

  2014cited by this paper
• The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light

  2014cited by this paper
• Circadian clocks and feeding time regulate the oscillations and levels of hepatic triglycerides.

  2014cited by this paper
• Circadian clock circuitry in colorectal cancer.

  2014cited by this paper
• Circadian properties of cancer stem cells in glioma cell cultures and tumorspheres.

  2014cited by this paper
• Circadian molecular clocks and cancer.

  2014cited by this paper
• Spatiotemporal separation of PER and CRY posttranslational regulation in the mammalian circadian clock

  2014influential reference
• Prognostic relevance of Period1 (Per1) and Period2 (Per2) expression in human gastric cancer.

  2014cited by this paper
• Deregulated expression of circadian clock genes in gastric cancer

  2014cited by this paper
• A positive role for PERIOD in mammalian circadian gene expression.

  2014cited by this paper
• Circadian clock gene expression regulates cancer cell growth through glutaminase.

  2014cited by this paper
• Cross-talk between the circadian clock and the cell cycle in cancer

  2014cited by this paper
• Running for time: circadian rhythms and melanoma

  2014cited by this paper
• Circadian clock proteins and immunity.

  2014cited by this paper
• Epigenetic control and the circadian clock: linking metabolism to neuronal responses.

  2014cited by this paper
• The E3 ubiquitin ligase UBE3A is an integral component of the molecular circadian clock through regulating the BMAL1 transcription factor

  2014cited by this paper
• Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut

  2014cited by this paper
• Deciphering molecular determinants of chemotherapy in gastrointestinal malignancy using systems biology approaches.

  2014cited by this paper
• Machine Learning Helps Identify CHRONO as a Circadian Clock Component

  2014cited by this paper
• PER1 phosphorylation specifies feeding rhythm in mice.

  2014cited by this paper
• Effects of chronic jet lag on the central and peripheral circadian clocks in CBA/N mice

  2014cited by this paper
• Depletion of White Adipose Tissue in Cancer Cachexia Syndrome Is Associated with Inflammatory Signaling and Disrupted Circadian Regulation

  2014cited by this paper
• Clock genes: their role in colorectal cancer.

  2014influential reference
• Epigenetics of Sleep and Chronobiology

  2014cited by this paper
• A Circadian Clock Gene, Rev-erbα, Modulates the Inflammatory Function of Macrophages through the Negative Regulation of Ccl2 Expression

  2014cited by this paper
• The circadian clock regulates rhythmic activation of the NRF2/glutathione-mediated antioxidant defense pathway to modulate pulmonary fibrosis

  2014cited by this paper
• The day/night proteome in the murine heart.

  2014cited by this paper
• Association between CLOCK, PER3 and CCRN4L with non‑small cell lung cancer in Brazilian patients.

  2014cited by this paper
• In-Vivo Quantitative Proteomics Reveals a Key Contribution of Post-Transcriptional Mechanisms to the Circadian Regulation of Liver Metabolism

  2014cited by this paper
• Egr1 regulates lithium-induced transcription of the Period 2 (PER2) gene.

  2013cited by this paper
• Melatonin enhances DNA repair capacity possibly by affecting genes involved in DNA damage responsive pathways

  2013cited by this paper
• Metastasis-associated protein 1 is an integral component of the circadian molecular machinery

  2013cited by this paper
• A Prader–Willi locus lncRNA cloud modulates diurnal genes and energy expenditure

  2013cited by this paper
• An association between clock genes and clock‐controlled cell cycle genes in murine colorectal tumors

  2013cited by this paper
• Shift work, circadian gene variants and risk of breast cancer.

  2013cited by this paper
• A Novel Link Between Circadian Clocks and Adipose Tissue Energy Metabolism

  2013cited by this paper
• Impaired leukocyte trafficking and skin inflammatory responses in hamsters lacking a functional circadian system.

  2013cited by this paper
• A Disruption Mechanism of the Molecular Clock in a MPTP Mouse Model of Parkinson’s Disease

  2013cited by this paper
• A circadian clock transcription model for the personalization of cancer chronotherapy.

  2013cited by this paper
• Interactions between endocrine and circadian systems.

  2013cited by this paper
• Systems biology modeling of omics data: effect of cyclosporine a on the Nrf2 pathway in human renal cells

  2013cited by this paper
• Circadian clocks and tumor biology: what is to learn from human skin biopsies?

  2013cited by this paper
• Overexpression of the Circadian Clock Gene Bmal1 Increases Sensitivity to Oxaliplatin in Colorectal Cancer

  2013cited by this paper
• hClock gene expression in human colorectal carcinoma.

  2013cited by this paper
• DNA methylation of the BMAL1 promoter.

  2013cited by this paper
• Detailed characterization of multiple myeloma circulating tumor cells shows unique phenotypic, cytogenetic, functional, and circadian distribution profile.

  2013cited by this paper
• Circadian transcriptome analysis in human fibroblasts from Hunter syndrome and impact of iduronate-2-sulfatase treatment

  2013cited by this paper
• Circadian pathway genes in relation to glioma risk and outcome

  2013cited by this paper
• Loss of corepressor PER2 under hypoxia up-regulates OCT1-mediated EMT gene expression and enhances tumor malignancy

  2013cited by this paper
• Quantitative peptidomics for discovery of circadian-related peptides from the rat suprachiasmatic nucleus.

  2013cited by this paper
• DBC1 (Deleted in Breast Cancer 1) modulates the stability and function of the nuclear receptor Rev-erbα

  2013cited by this paper
• Deficiency in PER proteins has no effect on the rate of spontaneous and radiation-induced carcinogenesis

  2013cited by this paper
• Circadian gene Clock contributes to cell proliferation and migration of glioma and is directly regulated by tumor‐suppressive miR‐124

  2013cited by this paper
• Bmal1 suppresses cancer cell invasion by blocking the phosphoinositide 3-kinase-Akt-MMP-2 signaling pathway

  2013cited by this paper
• Over‐expression of circadian clock gene Bmal1 affects proliferation and the canonical Wnt pathway in NIH‐3T3 cells

  2013cited by this paper
• Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

  2013cited by this paper
• Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

  2013cited by this paper
• The Circadian Binding of CLOCK Protein to the Promoter of C/ebpα Gene in Mouse Cells

  2013cited by this paper
• Effects of insufficient sleep on circadian rhythmicity and expression amplitude of the human blood transcriptome

  2013cited by this paper
• Comparing Label-Free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus

  2013cited by this paper
• Time recall; future concept of chronomodulating chemotherapy for cancer.

  2013cited by this paper
• The circadian rhythm in adult attention-deficit/hyperactivity disorder: current state of affairs

  2013cited by this paper
• Circadian clock regulates the host response to Salmonella

  2013cited by this paper
• Exploitation of host clock gene machinery by hepatitis viruses B and C.

  2013cited by this paper
• Circadian rhythms in insect disease vectors

  2013cited by this paper
• Toll-Like Receptor 7 Agonists: Chemical Feature Based Pharmacophore Identification and Molecular Docking Studies

  2013cited by this paper
• Mechanisms of rapid antidepressant effects of sleep deprivation therapy: clock genes and circadian rhythms.

  2013cited by this paper
• [Association of genetic variantions of circadian clock genes and risk of breast cancer].

  2013cited by this paper
• The role of circadian rhythm in breast cancer.

  2013cited by this paper
• Circadian clock characteristics are altered in human thyroid malignant nodules.

  2013cited by this paper
• Expression of phosphodiesterase 6 (PDE6) in human breast cancer cells

  2013cited by this paper
• Altered feeding differentially regulates circadian rhythms and energy metabolism in liver and muscle of rats.

  2013cited by this paper
• Association of the clock genes polymorphisms with colorectal cancer susceptibility

  2013cited by this paper
• Glucose sensor O-GlcNAcylation coordinates with phosphorylation to regulate circadian clock.

  2013cited by this paper
• Article Circadian Disruption Leads to Insulin Resistance and Obesity

  2013cited by this paper
• Development of Transgenic Minipigs with Expression of Antimorphic Human Cryptochrome 1

  2013cited by this paper
• Identifying Molecular Targets of Lifestyle Modifications in Colon Cancer Prevention

  2013cited by this paper
• Cryptochrome 1 Overexpression Correlates with Tumor Progression and Poor Prognosis in Patients with Colorectal Cancer

  2013cited by this paper
• CLOCK is a substrate of SUMO and sumoylation of CLOCK upregulates the transcriptional activity of estrogen receptor-α

  2013cited by this paper
• Circadian acetylome reveals regulation of mitochondrial metabolic pathways

  2013cited by this paper
• The circadian clock circuitry and the AHR signaling pathway in physiology and pathology.

  2013cited by this paper
• Potential cancer-related role of circadian gene TIMELESS suggested by expression profiling and in vitro analyses

  2013cited by this paper
• MicroRNA-185 oscillation controls circadian amplitude of mouse Cryptochrome 1 via translational regulation

  2013cited by this paper
• Posttranscriptional regulation of PER1 underlies the oncogenic function of IREα.

  2013cited by this paper
• A novel association of two non-synonymous polymorphisms in PER2 and PER3 genes with specific diurnal preference subscales.

  2013cited by this paper
• Central nervous system control of metabolism

  2012cited by this paper
• The oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs.

  2012cited by this paper
• Overlapping prefrontal systems involved in cognitive and emotional processing in euthymic bipolar disorder and following sleep deprivation: a review of functional neuroimaging studies.

  2012cited by this paper
• Casein Kinase 1 Proteomics Reveal Prohibitin 2 Function in Molecular Clock

  2012cited by this paper
• Human blood metabolite timetable indicates internal body time

  2012cited by this paper
• Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression

  2012influential reference
• Report s in a Mouse Model of Schizophrenia

  2012cited by this paper
• Regulation of circadian behavioral output via a MicroRNA-JAK/STAT circuit.

  2012cited by this paper
• The circadian clock controls toll-like receptor 9-mediated innate and adaptive immunity.

  2012cited by this paper
• Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

  2012cited by this paper
• Adult attention-deficit hyperactivity disorder is associated with alterations in circadian rhythms at the behavioural, endocrine and molecular levels

  2012cited by this paper
• Transcriptome Comparison between Fetal and Adult Mouse Livers: Implications for Circadian Clock Mechanisms

  2012cited by this paper
• Entrainment of breast (cancer) epithelial cells detects distinct circadian oscillation patterns for clock and hormone receptor genes

  2012cited by this paper

• Circadian genes and non-coding RNAs: interactions and implications in cancer

  2025cites this paper
• Circadian rhythm genes in cancer: insight into their functions and regulation involving noncoding RNAs

  2021influential citation
• Oscillatory release cycles of permissive dimensions in carcinogenesis

  2017cites this paper
• Nutritional systems biology of type 2 diabetes

  2015cites this paper