The circadian clock transcriptional complex: metabolic feedback intersects with epigenetic control

Masri, Selma; Zocchi, Loredana; Katada, Sayako; Mora, Eugenio Meza; Sassone–Corsi, Paolo

doi:10.1111/j.1749-6632.2012.06649.x

Cited by 51 publications

(39 citation statements)

References 62 publications

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“…Rhythmic oscillation of H3 acetylation and H3K4me2/me3 is reported to be positively related to rhythmic transcriptions of light/dark cycle-related genes, whereas H3K36me2 has a negative correlation [88]. Circadian rhythmic oscillation of histone modifications also were observed in mammals [32,89,90]. Using ChIP-seq and the expression tiling array, exact opposite rhythmic oscillations of such antagonistic marks (H3K4me3 and H3K9me3) have been found, with good correlation with the rhythmic transcriptions of circadian clock-related genes.…”

Section: A Specific Examples Of Exposures and Effects On Histone Modmentioning

confidence: 92%

Histone Modification Patterns and Their Responses to Environment

Dai

Wang

2014

Curr Envir Health Rpt

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Histone modifications play important roles in the epigenetic regulation of gene expression. Recent genomewide profiling of histone modifications with deep sequencingbased methods provides novel insights of crosstalk between histone modifications, leading to recent proposals of histone "language" or "web" as an alternative of "code" to appreciate combinatorial modification patterns. Environmental factor-altered histone modifications now may be addressed dynamically and systematically with the recognition and use of these interesting combinatorial patterns.

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Section: A Specific Examples Of Exposures and Effects On Histone Modmentioning

confidence: 92%

Histone Modification Patterns and Their Responses to Environment

Dai

Wang

2014

Curr Envir Health Rpt

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“…In peripheral tissues, the molecular clock regulates nutrient uptake, metabolism, energy storage, mitochondria biosynthesis and intracellular redox levels by targeting key metabolic genes including those controlling the Warburg effect, such as glucose-6-phosphatase, pyruvate kinase and glucose transporter 2 (GLUT) 17,20,179,259,260 . It also responds to food cues and nutrient sensors to shift metabolic balance independent of SCN clock function 12,261–266 .…”

Section: The Role Of the Mammalian Circadian Clock In Tumor Suppressionmentioning

confidence: 99%

The Circadian Clock in Cancer Development and Therapy

Kettner

2013

Progress in Molecular Biology and Translational Science

219

198

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Most aspects of mammalian function display circadian rhythms driven by an endogenous clock. The circadian clock is operated by genes and comprises a central clock in the brain that responds to environmental cues and controls subordinate clocks in peripheral tissues via circadian output pathways. The central and peripheral clocks coordinately generate rhythmic gene expression in a tissue-specific manner in vivo to couple diverse physiological and behavioral processes to periodic changes in the environment. However, as the world industrialized, activities that disrupt endogenous homeostasis with external circadian cues have increased. This change in lifestyle has been linked to increased risk of diseases in all aspects of human health, including cancer. Studies in humans and animal models have revealed that cancer development in vivo is closely associated with the loss of circadian homeostasis in energy balance, immune function and aging that are supported by cellular functions important for tumor suppression including cell proliferation, senescence, metabolism and DNA damage response. The clock controls these cellular functions both locally in cells of peripheral tissues and at the organismal level via extracellular signaling. Thus, the hierarchical mammalian circadian clock provides a unique system to study carcinogenesis as a deregulated physiological process in vivo. The asynchrony between host and malignant tissues in cell proliferation and metabolism also provides new and exciting options for novel anti-cancer therapies.

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“…The basic mechanisms causing transcriptional rhythms of the core clock components are similar among all tissues, but how tissue-specific circadian output is achieved remains unknown, although several mechanisms have been proposed (2). Among these are the use of tissue-specific transcription factors (TFs) or coregulators (6,8) and different temporal control of RNA polymerase II recruitment (9,10), as well as defined rhythms in histone modifications accompanied by differential gene regulation (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19).…”

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Identifying Novel Transcriptional Regulators with Circadian Expression

Schick

Becker

Thakurela

et al. 2016

Molecular and Cellular Biology

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Organisms adapt their physiology and behavior to the 24-h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops that are important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of downstream genes, resulting in their circadian expression. Despite progress in understanding circadian gene expression, only a few players involved in circadian transcriptional regulation, including transcription factors, epigenetic regulators, and long noncoding RNAs, are known. Aiming to discover such genes, we performed a high-coverage transcriptome analysis of a circadian time course in murine fibroblast cells. In combination with a newly developed algorithm, we identified many transcription factors, epigenetic regulators, and long intergenic noncoding RNAs that are cyclically expressed. In addition, a number of these genes also showed circadian expression in mouse tissues. Furthermore, the knockdown of one such factor, Zfp28, influenced the core clock network. Mathematical modeling was able to predict putative regulator-effector interactions between the identified circadian genes and may help for investigations into the gene regulatory networks underlying circadian rhythms.O rganisms adapt to the 24-h day-night cycle, which leads to oscillations in physiology and behavior. This is coordinated by an intrinsic molecular clock originating from the interplay of transcriptional-translational feedback loops (1). In mammals, the core loop consists of the transcriptional activators Clock and Bmal1 and the repressors Period (Per) and cryptochrome (Cry). In a second loop, retinoid-related orphan receptors (ROR) activate transcription while Rev-Erb factors (Nr1d1 and Nr1d2) repress transcription (2). These core clock components also regulate the expression of additional genes, possibly resulting in an oscillating transcription of these socalled clock-controlled genes and finally in the circadian phenotype.Recent genome-wide studies of circadian time courses in various mouse tissues indicated that each tissue expresses its own particular set of cyclical genes, which only partly overlap each other (3-7). Nearly half of all genes in the mouse genome show circadian oscillation in at least one tissue (7). The basic mechanisms causing transcriptional rhythms of the core clock components are similar among all tissues, but how tissue-specific circadian output is achieved remains unknown, although several mechanisms have been proposed (2). Among these are the use of tissue-specific transcription factors (TFs) or coregulators (6,8) and different temporal control of RNA polymerase II recruitment (9, 10), as well as defined rhythms in histone modifications accompanied by differential gene regulation (9-19).To gain further insight into the transcriptional control of the circadian rhythm, we aimed to identify novel factors, particularly transcription factors and epigenetic regula...

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The circadian clock transcriptional complex: metabolic feedback intersects with epigenetic control

Cited by 51 publications

References 62 publications

Histone Modification Patterns and Their Responses to Environment

Histone Modification Patterns and Their Responses to Environment

The Circadian Clock in Cancer Development and Therapy

Identifying Novel Transcriptional Regulators with Circadian Expression

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