An intrinsically disordered region controlling condensation of a circadian clock component and rhythmic transcription in the liver

Molecular Cell, Год журнала: 2023, Номер 83(19), С. 3457 - 3469.e7

Опубликована: Окт. 1, 2023

Язык: Английский

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Clock-dependent chromatin accessibility rhythms regulate circadian transcription

PLoS Genetics, Год журнала: 2024, Номер 20(5), С. e1011278 - e1011278

Опубликована: Май 28, 2024

Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made understanding regulatory clock proteins circadian rhythms, how chromatin affects rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible with Sequencing) on FAC-sorted Drosophila neurons assess genome-wide at dawn and dusk over cycle. We observed oscillations promoter enhancer regions hundreds genes, enhanced either or dawn, which correlated their peak transcriptional activity. Notably, genes were enriched E-box motifs, while those more accessible VRI/PDP1-box indicating that they are regulated core feedback loops, PER/CLK VRI/PDP1, respectively. Further, complete loss per 01 null mutants, consistently both dusk, underscoring critical Period protein driving compaction during repression phase dawn. Together, this study demonstrates regulation, revealing interplay between structure orchestrates precise timing biological processes throughout day. This work further implies variations might play central generation diverse expression patterns neurons.

Язык: Английский

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Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock

eLife, Год журнала: 2024, Номер 12

Опубликована: Март 25, 2024

Circadian clocks are composed of transcription-translation negative feedback loops that pace rhythms gene expression to the diurnal cycle. In filamentous fungus Neurospora crassa, proteins F requency ( RQ), RQ-interacting RNA helicase (FRH), and C asein-Kinase I (CK1) form FFC complex represses genes activated by white-collar (WCC). FRQ orchestrates key molecular interactions clock despite containing little predicted tertiary structure. Spin labeling pulse-dipolar electron spin resonance spectroscopy provide domain-specific structural insights into 989-residue intrinsically disordered FFC. contains a compact core associates organizes FRH CK1 coordinate their roles in WCC repression. phosphorylation increases conformational flexibility alters oligomeric state, but changes structure dynamics non-uniform. Full-length undergoes liquid–liquid phase separation (LLPS) sequester influence enzymatic activity. Although favors LLPS, LLPS feeds back reduce at higher temperatures. Live imaging hyphae reveals foci characteristic condensates near nuclear periphery. Analogous repressor organisms share position-specific sequence identity with FRQ; yet, they contain amino acid compositions promote LLPS. Hence, condensate formation may be conserved feature eukaryotic clocks.

Язык: Английский

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Coenzyme I and Biological Rhythm

Опубликована: Янв. 1, 2025

Язык: Английский

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Transcriptome and Metabolome Analyses Reveal Perfluorooctanoic Acid-Induced Kidney Injury by Interfering with PPAR Signaling Pathway

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(14), С. 11503 - 11503

Опубликована: Июль 15, 2023

Perfluorooctanoic acid (PFOA) is widely used in aviation science and technology, transportation, electronics, kitchenware, other household products. It stable the environment has potential nephrotoxicity. To investigate effect of PFOA exposure during pregnancy on kidneys offspring mice, a total 20 mice at day 0 gestation were randomly divided into two groups (10 each group), group was administered 0.2 mL dose 3.5 mg/kg or deionized water by gavage gestation. The kidney weight, index, histopathological observation, serum biochemistry, transcriptomics, metabolomics 35-day analyzed. In addition, malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT) levels measured. Transcriptome analysis results showed that 387 genes up-regulated 283 down-regulated compared with control group. These differentially expressed (DEGs) mainly concentrated peroxisome-proliferator-activated receptor (PPAR) signaling pathway circadian rhythm. Compared group, 64 73 metabolites up- down-regulated, respectively, altered enriched biosynthesis unsaturated fatty acids. can affect expression rhythm-related this change influenced PPAR pathway. causes oxidative stress kidneys, which responsible for significant changes associated

Язык: Английский

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Phosphorylation Promotes the Accumulation of PERIOD Protein Foci

Research, Год журнала: 2023, Номер 6

Опубликована: Янв. 1, 2023

Circadian clock drives the 24-h rhythm in our behavior and physiology. The molecular consists of a series transcriptional/translational feedback loops operated by number genes. A very recent study reported that protein PERIOD (PER) is organized into discrete foci at nuclear envelope fly circadian neurons, which believed to be important for controlling subcellular localization Loss inner membrane lamin B receptor (LBR) leads disruption these foci, but how they are regulated yet unknown. Here, we found PER likely phase-separated condensates, formation mediated intrinsically disordered region PER. Phosphorylation promotes accumulation foci. Protein phosphatase 2A, known dephosphorylate PER, hampers On other hand, kinase DOUBLETIME (DBT) phosphorylates enhances LBR facilitates destabilizing catalytic subunit MICROTUBULE STAR (MTS). In conclusion, here, demonstrate key role phosphorylation promoting while modulates this process impinging on MTS.

Язык: Английский

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PRD-2 mediates clock-regulated perinuclear localization of clock gene RNAs within the circadian cycle of Neurospora

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(31)

Опубликована: Июль 26, 2022

The transcription–translation negative feedback loops underlying animal and fungal circadian clocks are remarkably similar in their molecular regulatory architecture and, although much is understood about central mechanism, little known the spatiotemporal dynamics of gene products involved. A common feature these oscillators a significant temporal delay between rhythmic accumulation clock messenger RNAs (mRNAs) encoding arm proteins, for example, frq Neurospora Per1-3 mammals, appearance protein complexes assembled from proteins they encode. Here, we report use single-molecule RNA fluorescence situ hybridization (smFISH) to show that fraction nuclei actively transcribing changes manner, mRNAs cycle abundance with fewer than five transcripts per nucleus at any time. Spatial point patterning statistics reveal spatially clustered near time day–dependent manner clustering requires an RNA-binding protein, PRD-2 (PERIOD-2), recently shown also bind mRNA another core component, casein kinase 1. An intrinsically disordered displays behavior vivo vitro consistent participation biomolecular condensates. These data role phase-separating spatiotemporally organizing facilitate local translation assembly complexes.

Язык: Английский

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Conformational changes in the negative arm of the circadian clock correlate with dynamic interactomes involved in post-transcriptional regulation

Cell Reports, Год журнала: 2023, Номер 42(4), С. 112376 - 112376

Опубликована: Апрель 1, 2023

Biology is tuned to the Earth's diurnal cycle by circadian clock, a transcriptional/translational negative feedback loop that regulates physiology via transcriptional activation and other post-transcriptional mechanisms. We hypothesize regulation might stem from conformational shifts in intrinsically disordered proteins comprise arm of coordinate variation negative-arm-centered macromolecular complexes. This work demonstrates temporal fluidity correlates with 24-h physiologically diverse complex components eukaryotic clock proteins. Short linear motifs on negative-arm correspond interactors localized regions known phosphorylation sites suggesting changes these complexes could be due imparted phospho-state. Interactors oscillate over time correlate post-transcriptionally regulated proteins, highlighting how time-of-day protein may tune cellular physiology.

Язык: Английский

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Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock

eLife, Год журнала: 2023, Номер 12

Опубликована: Ноя. 24, 2023

Circadian clocks are composed of transcription-translation negative feedback loops that pace rhythms gene expression to the diurnal cycle. In filamentous fungus Neurospora crassa, proteins Frequency (FRQ), FRQ-interacting RNA helicase (FRH), and Casein-Kinase I (CK1) form FFC complex represses genes activated by white-collar (WCC). FRQ orchestrates key molecular interactions clock despite containing little predicted tertiary structure. Spin labeling pulse-dipolar electron spin resonance spectroscopy provide domain-specific structural insights into 989-residue intrinsically disordered FFC. contains a compact core associates organizes FRH CK1 coordinate their roles in WCC repression. phosphorylation increases conformational flexibility alters oligomeric state, but changes structure dynamics non-uniform. Full-length undergoes liquid-liquid phase separation (LLPS) sequester influence enzymatic activity. Although favors LLPS, LLPS feeds back reduce at higher temperatures. Live imaging hyphae reveals foci characteristic condensates near nuclear periphery. Analogous repressor organisms share position-specific sequence identity with FRQ; yet, they contain amino acid compositions promote LLPS. Hence, condensate formation may be conserved feature eukaryotic clocks.

Язык: Английский

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Mammalian circadian clock proteins form dynamic interacting microbodies distinct from phase separation

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(52)

Опубликована: Дек. 21, 2023

Liquid–liquid phase separation (LLPS) underlies diverse biological processes. Because most LLPS studies were performed in vitro using recombinant proteins or cells that overexpress protein, the physiological relevance of for endogenous protein is often unclear. PERIOD, intrinsically disordered domain-rich proteins, are central mammalian circadian clock components and interact with other core negative feedback loop. Different previously shown to form large complexes. Circadian rely on experiments proteins. Here, we show when Per2 transgene was stably expressed cells, PER2 formed nuclear phosphorylation-dependent slow-moving condensates recruited Super-resolution microscopy PER2, however, revealed formation circadian-controlled, rapidly diffusing microbodies resistant concentration changes, hexanediol treatment, loss phosphorylation, indicating they distinct from caused by overexpression. Surprisingly, only a small fraction transiently BMAL1 CRY1, conclusion confirmed mice tissues, suggesting an enzyme-like mechanism process. Together, these results demonstrate dynamic interactions key feature importance examining studies.

Язык: Английский

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