Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study

Xue, Tuo; Song, Changcheng; Wang, Qing; Wang, Yan; Chen, Guangju

doi:10.1371/journal.pone.0155105

Cited by 8 publications

(7 citation statements)

References 80 publications

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“…The master clock is regulated by four major groups of genes: Clock, Bmal1, Cry ( Cryptochrome 1 and 2), and Per ( Period 1 and 2). These core circadian genes are regulated in a transcription-translation feedback loop (TTFL) (Xue et al, 2016). …”

Section: Introductionmentioning

confidence: 99%

Role of circadian gene Clock during differentiation of mouse pluripotent stem cells

et al. 2016

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Biological rhythms controlled by the circadian clock are absent in embryonic stem cells (ESCs). However, they start to develop during the differentiation of pluripotent ESCs to downstream cells. Conversely, biological rhythms in adult somatic cells disappear when they are reprogrammed into induced pluripotent stem cells (iPSCs). These studies indicated that the development of biological rhythms in ESCs might be closely associated with the maintenance and differentiation of ESCs. The core circadian gene Clock is essential for regulation of biological rhythms. Its role in the development of biological rhythms of ESCs is totally unknown. Here, we used CRISPR/CAS9-mediated genetic editing techniques, to completely knock out the Clock expression in mouse ESCs. By AP, teratoma formation, quantitative real-time PCR and Immunofluorescent staining, we did not find any difference between Clock knockout mESCs and wild type mESCs in morphology and pluripotent capability under the pluripotent state. In brief, these data indicated Clock did not influence the maintaining of pluripotent state. However, they exhibited decreased proliferation and increased apoptosis. Furthermore, the biological rhythms failed to develop in Clock knockout mESCs after spontaneous differentiation, which indicated that there was no compensational factor in most peripheral tissues as described in mice models before (DeBruyne et al., 2007b). After spontaneous differentiation, loss of CLOCK protein due to Clock gene silencing induced spontaneous differentiation of mESCs, indicating an exit from the pluripotent state, or its differentiating ability. Our findings indicate that the core circadian gene Clock may be essential during normal mESCs differentiation by regulating mESCs proliferation, apoptosis and activity.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-016-0319-9) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Role of circadian gene Clock during differentiation of mouse pluripotent stem cells

et al. 2016

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“…For instance, the biological influence of photoperiod may reside in that it modulates the seasonal changes in night length, which is negatively correlated with the melatonin concentration in blood 33–36 . At the cellular level, the biological clock that regulates the cyclicity of somatic cell is governed by the expression of specific genes 37 . Since the spermatozoon is a transcriptionally inactive cell, another system may operate.…”

Section: Discussionmentioning

confidence: 99%

Sperm physiology varies according to ultradian and infradian rhythms

Moreno-Irusta

Kembro

Domïnguez

et al. 2019

Sci Rep

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The spermatozoon must be physiologically prepared to fertilize the egg, process called capacitation. Human sperm samples are heterogeneous in their ability to capacitate themselves, which leads to variability between samples from the same or different donors, and even along the seasons. Here we studied sperm variation in the capacitation state according to the ability of capacitated spermatozoa to acrosome react upon stimulation (% ARi) and to be recruited by chemotaxis (% Chex). Both indirect indicators of sperm capacitation increased along the incubation time with fluctuations. Those capacitated sperm recruited by chemotaxis showed an ultradian rhythm with a cycle every 2 h, which might be influenced by unknown intrinsic sperm factors. Two infradian rhythms of 12 months for the % ARi and of 6 months for % Chex were observed, which are associated with the joint action of temperature and photoperiod. Thus, to avoid false negative results, human sperm samples are recommended to be incubated for a long period (e.g. 18 h) preferably in spring time. This innovative point of view would lead to better comprehend human reproductive biology and to think experimental designs in the light of sperm cyclicity or to improve sperm aptitude for clinical purposes.

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“…Infradian rhythms were observed in testis function [ 222 ], semen quality [ 223 ] and some parameters of sperm physiology such as acrosome reaction (a 12 months cycle) and chemotaxis (a 6 month cycle) [ 30 ]. The cyclicity of the biological clock of somatic cells is regulated by specific genes [ 224 ]. However, the spermatozoans are transcriptionally inactive cells and therefore the presence of some molecules such as melatonin in the seminal plasma may regulate the variations observed in sperm physiology [ 225 ].…”

Section: 3p Medicine and Variationsmentioning

confidence: 99%

Physiological Rhythms and Biological Variation of Biomolecules: The Road to Personalized Laboratory Medicine

Coşkun

Zarepour

Zarrabi

2023

IJMS

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The concentration of biomolecules in living systems shows numerous systematic and random variations. Systematic variations can be classified based on the frequency of variations as ultradian (<24 h), circadian (approximately 24 h), and infradian (>24 h), which are partly predictable. Random biological variations are known as between-subject biological variations that are the variations among the set points of an analyte from different individuals and within-subject biological variation, which is the variation of the analyte around individuals’ set points. The random biological variation cannot be predicted but can be estimated using appropriate measurement and statistical procedures. Physiological rhythms and random biological variation of the analytes could be considered the essential elements of predictive, preventive, and particularly personalized laboratory medicine. This systematic review aims to summarize research that have been done about the types of physiological rhythms, biological variations, and their effects on laboratory tests. We have searched the PubMed and Web of Science databases for biological variation and physiological rhythm articles in English without time restrictions with the terms “Biological variation, Within-subject biological variation, Between-subject biological variation, Physiological rhythms, Ultradian rhythms, Circadian rhythm, Infradian rhythms”. It was concluded that, for effective management of predicting, preventing, and personalizing medicine, which is based on the safe and valid interpretation of patients’ laboratory test results, both physiological rhythms and biological variation of the measurands should be considered simultaneously.

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Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study

Cited by 8 publications

References 80 publications

Role of circadian gene Clock during differentiation of mouse pluripotent stem cells

Role of circadian gene Clock during differentiation of mouse pluripotent stem cells

Sperm physiology varies according to ultradian and infradian rhythms

Physiological Rhythms and Biological Variation of Biomolecules: The Road to Personalized Laboratory Medicine

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