Genome-wide circadian regulation: A unique system for computational biology

Lingying Sun; Junjie Ma; Christoph W Turck; Pin Xu; Guang-Zhong Wang

doi:10.1016/j.csbj.2020.07.002

Genome-wide circadian regulation: A unique system for computational biology

Comput Struct Biotechnol J. 2020 Jul 10:18:1914-1924. doi: 10.1016/j.csbj.2020.07.002. eCollection 2020.

Authors

Lingying Sun¹, Junjie Ma¹, Christoph W Turck², Pin Xu³, Guang-Zhong Wang¹

Affiliations

¹ CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
² Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich 80804, Germany.
³ Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA.

Abstract

Circadian rhythms are 24-hour oscillations affecting an organism at multiple levels from gene expression all the way to tissues and organs. They have been observed in organisms across the kingdom of life, spanning from cyanobacteria to humans. In mammals, the master circadian pacemaker is located in the hypothalamic suprachiasmatic nuclei (SCN) in the brain where it synchronizes the peripheral oscillators that exist in other tissues. This system regulates the circadian activity of a large part of the transcriptome and recent findings indicate that almost every cell in the body has this clock at the molecular level. In this review, we briefly summarize the different factors that can influence the circadian transcriptome, including light, temperature, and food intake. We then summarize recently identified general principles governing genome-scale circadian regulation, as well as future lines of research. Genome-scale circadian activity represents a fascinating study model for computational biology. For this purpose, systems biology methods are promising exploratory tools to decode the global regulatory principles of circadian regulation.

Keywords: ABSR, Autoregressive Bayesian spectral regression; AMPK, AMP-activated protein kinase; AR, Arrhythmic feeding; ARSER, Harmonic regression based on autoregressive spectral estimation; BMAL1, The aryl hydrocarbon receptor nuclear translocator-like (ARNTL); CCD, Cortical collecting duct; CR, Calorie-restricted diet; CRY, Cryptochrome; Circadian regulatory network; Circadian rhythms; Circadian transcriptome; Cycling genes; DCT/CNT, Distal convoluted tubule and connecting tubule; DD, Dark: dark; Energetic cost; HF, High fat diet; JTK_CYCLE, Jonckheere-Terpstra-Kendall (JTK) cycle; KD, Ketogenic diet; LB, Ad libitum; LD, Light:dark; LS, Lomb-Scargle; Liver-RE, Liver clock reconstituted BMAL1-deficient mice; NAD, Nicotinamide adenine dinucleotides; ND, Normal diet; NR, Night-restricted feeding; PAS, PER-ARNT-SIM; PER, Period; RAIN, Rhythmicity Analysis Incorporating Nonparametric methods; RF, Restricted feeding; SCN, Suprachiasmatic nucleus; SREBP, The sterol regulatory element binding protein; TTFL, Transcriptional-translational feedback loop; WT, Wild type; eJTK_CYCLE, Empirical JTK_CYCLE.

Publication types

Review