The phase-shifting effect of bright light exposure on circadian rhythmicity in the human transcriptome
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PROVIDER: PRJNA506081 | ENA |
REPOSITORIES: ENA
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Project description:Eleven healthy human subjects were enrolled in a 6-day simulated shift work protocol. Blood samples were collected during the two 24-hour measurement periods. Blood samples were collected every 4 hours during both measurement periods. Subjects entered the lab on Day 1. At the start of Day 2, the first 24-hour measurement period was started. Subjects slept according to their habitual sleep/wake schedule, followed by a 16-hour constant posture procedure. On days 3-6, the sleep period was delayed by 10 hours. Participants in the control group were exposed to dim light throughout the waking periods; participants in the bright group were exposed to bright light (~6,000lux) for 8 hours during the waking period. Following the third night on this schedule, subjects underwent another 24-hour measurement period. During both measurement periods, blood samples were collected and PBMCs were isolated. mRNA was extracted, labelled, and hybridized to microarrays.
2019-02-14 | GSE122725 | GEO
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Project description:Background. Inter- and intra-individual fluctuations in pain intensity pose a major challenge to treatment efficacy, with a majority perceiving their pain relief as inadequate. Recent preclinical studies have identified circadian rhythmicity as a potential contributor to these fluctuations and therapeutic target. Methods. We therefore sought to determine the impact of these rhythms in people with chronic low back pain (CLBP) through a detailed characterization, including questionnaires to evaluate biopsychosocial characteristics, ecological momentary assessment (7-day e-diaries at 8:00/14:00/20:00) to assess pain fluctuations, and intra-day blood transcriptomics (8:00/20:00) to identify genes/pathways of interest. Results. While most individuals displayed constant or variable/mixed pain phenotypes, a distinct subset had daily fluctuations of increasing pain scores (>30% change in intensity over 12-hours in ≥4/7 days). This population had no opioid users, better biopsychosocial profiles, and differentially expressed transcripts relative to other pain phenotypes. The circadian-governed neutrophil degranulation pathway was particularly enriched among arhythmic individuals; the link between neutrophil degranulation and opioid use was further confirmed in a separate CLBP cohort. Conclusion. Our findings identify pain rhythmicity and the circadian expression of neutrophil degranulation pathways as indicators of CLBP outcomes, which may help provide a personalized approach to phenotyping biopsychosocial characteristics and medication use. This highlights the need to better understand the impact of circadian rhythmicity across chronic pain conditions.
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Project description:Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves fine tuning between transcriptional and post-transcriptional molecular mechanisms, strongly dependent on the metabolic state of the cell, which guarantees adaptive plasticity of tissue-specific genetic programs. Dynamics of epigenome structure and epigenetic regulators support this plasticity. However, the intermingle between epigenome and RNA Pol II rhythmicity remains to be investigated. Here we identify the Polycomb group (PcG) protein EZH1 as a gateway bridging function regulating periodic alternation between chromatin mediated silencing and active transcription in post-mitotic skeletal muscle cells. We show that PRC2-EZH1 core components are under direct regulation of BMAL1, and show an oscillatory behavior and a regulated periodic assembly of PRC2-EZH1 complex. Instead at alternate Zeitgeber points, EZH1 becomes essential for circadian gene expression, through stabilization of RNA Pol II preinitiation complex controlling nascent transcription process. Collectively, our data show that EZH1 depending on the stoichiometry of its partners guarantees both negative and positive modulation of RNA Pol II activity, resulting in oscillatory transcription.
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Project description:Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves the fine tuning between transcriptional and post-transcriptional molecular mechanisms, strongly dependent on the metabolic state of the cell that guarantees intrinsic plasticity of tissue specific genetic programs. To support the plastic properties a key role is played by the dynamics of epigenome structure and its regulators. Here we investigate the role of the Polycomb cell memory complex PRC2-EZH1 in regulating transcriptional rhythmicity in post-mitotic skeletal muscle cells. We show that PRC2-EZH1 core components are under direct regulation of BMAL1, show an oscillatory behavior and control both silencing and activation of target genes. Fully assembled PRC2-EZH1 complex negatively regulates cyclic expression of direct targets through modulation of cyclic H3K27me3 status. Conversely, we show that EZH1 regulates constitutive circadian genes expression, through stabilization of RNA Pol II machinery and maintenance of transcription process fidelity. Collectively, these findings unveil the dual and multi role of PcG in circadian gene regulation in adult skeletal muscle cells, and the plastic nature of PcG cell memory system in somatic cells.
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Project description:Humans have a circadian rhythm for which the period varies among individuals. In the present study, we investigated the amount of natural phase delay of circadian rhythms after spending a day under dim light (Day 1 to Day 2) and the amount of phase advance due to light exposure (8000 lx, 4100 K) the following morning (Day 2 to Day 3). The relationships of the phase shifts with the circadian phase, chronotype and sleep habits were also investigated. Dim light melatonin onset (DLMO) was investigated as a circadian phase marker on each day. In the 27 individuals used for the analysis, DLMO was delayed significantly (-0.24 ± 0.33 h, p < 0.01) from Day 1 to Day 2 and DLMO was advanced significantly (0.18 ± 0.36 h, p < 0.05) from Day 2 to Day 3. There was a significant correlation between phase shifts, with subjects who had a greater phase delay in the dim environment having a greater phase advance by light exposure (r = -0.43, p < 0.05). However, no significant correlations with circadian phase, chronotype or sleep habits were found. These phase shifts may reflect the stability of the phase, but do not account for an individual's chronotype-related indicators.
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Project description:Circadian clocks are essential for generating and coordinating rhythms in animals’ physiology, behaviour, and metabolism. These activities are regulated by intracellular molecular clocks that operate with a ~24 hour periodicity. The African striped mouse, Rhabdomys pumilio, is notable for undergoing temporal niche switching from ancestrally nocturnal to diurnal, although the molecular components of its’ circadian organization remain unknown. We undertook transcriptome profiling of daily rhythms in the suprachiasmatic nucleus (SCN) and in the liver, lung and retina of Rhabdomys stably housed under a stable 12h:12h light:dark cycle with bright (n=10) or dim (n=10) daytime light intensity. Tissues were collected at two time points: two hours after lights on (Zeitgeber Time (ZT2)) coinciding with high behavioural activity, or two hours after lights off (ZT14) during the animal’s resting/sleep period, and RNA-sequencing performed.
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Project description:A circadian clock is located in the retinal photoreceptors of the African clawed frog Xenopus laevis. These photoreceptor clocks are thought to govern a wide variety of output rhythms, including melatonin release and gene expression. Both light and dopamine phase shift the retinal clock in a phase-dependent manner. Two homologs of the Drosophila period gene have been cloned in Xenopus, and one of these (xPer2) is acutely regulated by light. Light and dopamine induce xPer2 mRNA in a similar manner. In addition, the increase of xPer2 mRNA in response to light and dopamine is the same at all times of day tested. In contrast, xPer1 mRNA exhibits circadian oscillations but is relatively insensitive to phase-shifting treatments of light or dopamine. Our data suggest that xPer2 functions as the molecular link between the light/dark cycle and the circadian clock.
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