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Discovering the Physiological Significance and Regulatory Mechanisms of Circadian Rhythm...
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Discovering the Physiological Significance and Regulatory Mechanisms of Circadian Rhythm Generation

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 6727

Special Issue Editor

Dr. Xiaodong Li

E-Mail Website
Guest Editor
College of Life Sciences, Wuhan University, Luojia Hill, Wuhan 430072, China
Interests: Pol II; mouse liver; regulation of temporal output of gene transcription; global pattern of pausing regulation

Special Issue Information

Dear Colleagues,

Internal biological clocks govern the timing of various physiological processes to generate circadian rhythms and are essential to the regulation of numerous aspects of an organism's life. These rhythms are crucial for coordinating various cellular functions, including metabolism, hormone secretion, immune response, and behavior, in alignment with the external day–night cycle.

In recent years, significant research progress has been made regarding the regulation of circadian gene expression rhythms. Circadian rhythms interact closely with various cellular functions in different cell types, thus requiring their operation to possess plasticity and specificity in different environments. Gene expression regulation involves multiple mechanisms at the transcriptional level (such as transcription factors, and many cofactors involved in histone modification and chromatin remodeling), as well as mechanisms at the post-transcriptional and metabolite levels, making it highly complex. How these mechanisms participate in the regulation of circadian rhythms awaits future research at the genomic scale, with their physiological significance also worthy of exploration.

This Special Issue aims to present recent advances and ongoing research on this topic in different species. It welcomes the submission of original research and review articles focusing on the regulatory mechanisms of circadian rhythms and their physiological significance.

Dr. Xiaodong Li
Guest Editor

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Keywords

  • circadian rhythms
  • biological clocks
  • chromatin
  • transcription
  • histone
  • nucleosome
  • pausing
  • pause release

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Published Papers (3 papers)

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Research

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18 pages, 3288 KiB  
Article
The Change Rate of the Fbxl21 Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals
by Vassily A. Lyubetsky, Gregory A. Shilovsky, Jian-Rong Yang, Alexandr V. Seliverstov and Oleg A. Zverkov
Biology 2024, 13(10), 792; https://doi.org/10.3390/biology13100792 - 2 Oct 2024
Viewed by 1923
Abstract
This article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species containing this [...] Read more.
This article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species containing this gene. The methodology is illustrated based on the mammalian genes responsible for regulating the circadian rhythms that underlie a number of human disorders, particularly those associated with aging. The methods used are statistical and bioinformatic ones. A systematic search for orthologues, pseudogenes, and gene losses was performed using our previously developed methods. It is demonstrated that the least conserved Fbxl21 gene in the Euarchontoglires superorder exhibits a statistically significant connection of genomic characteristics (the median of dN/dS for a gene relative to all the other orthologous genes of a taxon, as well as the preference or avoidance of certain amino acids in its protein) with species-specific lifespan and body weight. In contrast, no such connection is observed for Fbxl21 in the Laurasiatheria superorder. This study goes beyond the protein-coding genes, since the accumulation of amino acid substitutions in the course of evolution leads to pseudogenization and even gene loss, although the relationship between the genomic characteristics and the species traits is still preserved. The proposed methodology is illustrated using the examples of circadian rhythm genes and proteins in placental mammals, e.g., longevity is connected with the rate of Fbxl21 gene change, pseudogenization or gene loss, and specific amino acid substitutions (e.g., asparagine at the 19th position of the CRY-binding domain) in the protein encoded by this gene. Full article
(This article belongs to the Special Issue Discovering the Physiological Significance and Regulatory Mechanisms of Circadian Rhythm Generation)
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Review

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25 pages, 1602 KiB  
Review
Epigenetic Mechanisms in the Transcriptional Regulation of Circadian Rhythm in Mammals
by Wei Mao, Xingnan Ge, Qianping Chen and Jia-Da Li
Biology 2025, 14(1), 42; https://doi.org/10.3390/biology14010042 - 8 Jan 2025
Viewed by 2173
Abstract
Almost all organisms, from the simplest bacteria to advanced mammals, have
a near 24 h circadian rhythm. Circadian rhythms are highly conserved across different life forms and are regulated by circadian genes as well as by related transcription factors. Transcription factors are fundamental [...] Read more.
Almost all organisms, from the simplest bacteria to advanced mammals, have
a near 24 h circadian rhythm. Circadian rhythms are highly conserved across different life forms and are regulated by circadian genes as well as by related transcription factors. Transcription factors are fundamental to circadian rhythms, influencing gene expression, behavior in plants and animals, and human diseases. This review examines the foundational research on transcriptional regulation of circadian rhythms, emphasizing histone modifications, chromatin remodeling, and Pol II pausing control. These studies have enhanced our understanding of transcriptional regulation within biological circadian rhythms and the importance of circadian biology in human health. Finally, we summarize the progress and challenges in these three areas of regulation to move the field forward. Full article
(This article belongs to the Special Issue Discovering the Physiological Significance and Regulatory Mechanisms of Circadian Rhythm Generation)
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15 pages, 328 KiB  
Review
Circadian Regulation in Diurnal Mammals: Neural Mechanisms and Implications in Translational Research
by Yirun Jiang, Jiaming Shi, Jun Tai and Lily Yan
Biology 2024, 13(12), 958; https://doi.org/10.3390/biology13120958 - 22 Nov 2024
Cited by 2 | Viewed by 1650
Abstract
Diurnal and nocturnal mammals have evolved unique behavioral and physiological adaptations to optimize survival for their day- or night-active lifestyle. The mechanisms underlying the opposite activity patterns are not fully understood but likely involve the interplay between the circadian time-keeping system and various [...] Read more.
Diurnal and nocturnal mammals have evolved unique behavioral and physiological adaptations to optimize survival for their day- or night-active lifestyle. The mechanisms underlying the opposite activity patterns are not fully understood but likely involve the interplay between the circadian time-keeping system and various arousal- or sleep-promoting factors, e.g., light or melatonin. Although the circadian systems between the two chronotypes share considerable similarities, the phase relationships between the principal and subordinate oscillators are chronotype-specific. While light promotes arousal and wakefulness in diurnal species like us, it induces sleep in nocturnal ones. Similarly, melatonin, the hormone of darkness, is commonly used as a hypnotic in humans but is secreted in the active phase of nocturnal animals. Thus, the difference between the two chronotypes is more complex than a simple reversal, as the physiological and neurological processes in diurnal mammals during the day are not equivalent to that of nocturnal ones at night. Such chronotype differences could present a significant translational gap when applying research findings obtained from nocturnal rodents to diurnal humans. The potential advantages of diurnal models are being discussed in a few sleep-related conditions including familial natural short sleep (FNSS), obstructive sleep apnea (OSA), and Smith–Magenis syndrome (SMS). Considering the difference in chronotype, a diurnal model will be more adequate for revealing the physiology and physiopathology pertaining to human health and disease, especially in conditions in which circadian rhythm disruption, altered photic response, or melatonin secretion is involved. We hope the recent advances in gene editing in diurnal rodents will promote greater utility of the diurnal models in basic and translational research. Full article
(This article belongs to the Special Issue Discovering the Physiological Significance and Regulatory Mechanisms of Circadian Rhythm Generation)
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