The rhythmic transcriptional landscape inCaenorhabditis elegans: daily, circadian and novel 16-hour cycling gene expression revealed by RNA-sequencing DOI
Jack Munns, Katherine Newling, Sally James

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 7, 2024

Abstract The nematode Caenorhabditis elegans is an unconventional model in chronobiology, reported to exhibit physiological and behavioural circadian rhythms while lacking a defined transcriptional oscillator. extent importance of C. remain uncertain, given probable lack functional conservation key proteins, relatively non-robust ambiguous diel ecology. Here, we investigated the temporal coordination gene expression post-development using RNA sequencing. Over time series, which synchronised nematodes combined light temperature cycles, found clear evidence daily oscillations 343 genes JTK_Cycle. However, were not well-sustained constant conditions, with only 13 remaining significantly rhythmic. Reanalysis previous transcriptomic data echoed this finding identifying far fewer rhythmic also greater number overall. Weighted co-expression network analysis (WGCNA), hierarchical clustering approach, further confirmed prevalent environmentally driven RNA-seq data. This additionally revealed novel trend over 1000 exhibited hitherto unreported 16-hour oscillations, highlighting new facet .

Language: Английский

Circatidal control of gene expression in the deep-sea hot vent shrimp Rimicaris leurokolos DOI
Hongyin Zhang, Takuya Yahagi, Norio Miyamoto

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2040)

Published: Feb. 1, 2025

Biological clocks are a ubiquitous feature of all life, enabling the use natural environmental cycles to track time. Although studies on circadian rhythms have contributed greatly knowledge chronobiology, biological in dark biospheres such as deep sea remain poorly understood. Here, based free-running experiment laboratory, we reveal potentially endogenous gene expression deep-sea hydrothermal vent shrimp Rimicaris leurokolos . Oscillations with approximately 12 h periods, probably reflecting tidal influence, prevail over others temporal transcriptome, indicating R. depends circatidal clock consisting at least some components independent from clocks. The transcripts exhibit an antiphased pattern divided into two internally synchronized clusters, correlated wide-ranging processes that occur nucleus and cytoplasm, respectively. In addition, showed great similarities genes fruit flies mice exhibiting ultradian rhythms, tide had broad impact evolution oscillations found across Metazoa. These findings not only provide new insights adaptations organisms but also highlight intriguing models for chronobiological studies, particularly those linked rhythms.

Language: Английский

Citations

1
Circatidal control of gene expression in the deep-sea hot vent shrimpRimicaris leurokolos DOI Creative Commons
Hongyin Zhang, Takuya Yahagi, Norio Miyamoto

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 15, 2024

Abstract Biological clocks are a ubiquitous feature of all life, enabling the use natural environmental cycles to track time. Although studies on circadian rhythms have contributed greatly knowledge chronobiology, biological in dark biospheres such as deep sea remain poorly understood. Here, based laboratory free-running experiment, we reveal potentially endogenous gene expression deep-sea hydrothermal vent shrimp Rimicaris leurokolos . Oscillations with ∼12-hour periods, likely reflecting tidal influence, prevail over others temporal transcriptome, indicating R. depends circatidal clock consisting at least some components independent clocks. The transcripts exhibit an antiphased pattern divided into two internally synchronized clusters, correlated wide-ranging processes that occur nucleus and cytoplasm, respectively. In addition, comparing ultradian genes fruit flies mice shows large similarity, scenario broad impact tide oscillations across metazoan. These findings not only provide new insights adaptations organisms but also highlight intriguing models for chronobiological, particularly 12-hour rhythms, studies.

Language: Английский

Citations

2
Nuclear speckle rejuvenation alleviates proteinopathies at the expense of YAP1 DOI Creative Commons
William Dion,

Yuren Tao,

Maci Chambers

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 21, 2024

Abstract Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as pivotal membrane-less organelle responsible transcriptional control, we aim to alleviate proteinopathies through speckle rejuvenation. We identified pyrvinium pamoate small-molecule rejuvenator that enhances while suppressing YAP1 signaling via decreasing surface/interfacial tension condensates interaction with intrinsically disordered region scaffold SON. In pre-clinical models, nanomolar alleviated retina degeneration and reduced tauopathy by promoting autophagy ubiquitin-proteasome system SON-dependent manner without causing cellular stress. Aberrant morphology, increased activity were also observed human tauopathies. Our study uncovers novel therapeutic targets tackling misfolding disorders within an expanded framework encompassing YAP1.

Language: Английский

Citations

2
CircaKB: a comprehensive knowledgebase of circadian genes across multiple species DOI Creative Commons
Xingchen Zhu, Xiao Han, Zhijin Li

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D67 - D78

Published: Sept. 26, 2024

Abstract Circadian rhythms, which are the natural cycles that dictate various physiological processes over a 24-h period, have been increasingly recognized as important in management and treatment of human diseases. However, lack sufficient data reliable analysis methods major obstacle to understanding bidirectional interaction between circadian variation health. We developed CircaKB, comprehensive knowledgebase genes across multiple species. CircaKB is first provides systematic annotations oscillatory patterns gene expression at genome-wide level for 15 representative Currently, contains 226 time-course transcriptome datasets, covering wide variety tissues, organs, cell lines. In addition, integrates 12 computational models facilitate identify their variations expression. also offers powerful functionalities its users, including easy search, fast browsing, strong visualization, custom upload. believe will be valuable tool resource research community, contributing identification new targets disease prevention treatment. made freely accessible https://cdsic.njau.edu.cn/CircaKB.

Language: Английский

Citations

1
Epigenetic regulation of global proteostasis dynamics by RBBP5 ensures mammalian organismal health DOI Creative Commons
Syeda Kubra, Michelle Sun, William Dion

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 13, 2024

Proteostasis is vital for cellular health, with disruptions leading to pathologies including aging, neurodegeneration and metabolic disorders. Traditionally, proteotoxic stress responses were studied as acute reactions various noxious factors; however, recent evidence reveals that many proteostasis stress-response genes exhibit ∼12-hour ultradian rhythms under physiological conditions in mammals. These rhythms, driven by an XBP1s-dependent 12h oscillator, are crucial managing proteostasis. By exploring the chromatin landscape of murine hepatic we identified RBBP5, a key subunit COMPASS complex writing H3K4me3, essential epigenetic regulator RBBP5 indispensable regulating both oscillator transcriptional response stress, acting co-activator transcription factor XBP1s. ablation leads increased sensitivity chronic inflammation, steatosis mice, along impaired autophagy reduced cell survival

Language: Английский

Citations

0
The rhythmic transcriptional landscape inCaenorhabditis elegans: daily, circadian and novel 16-hour cycling gene expression revealed by RNA-sequencing DOI
Jack Munns, Katherine Newling, Sally James

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 7, 2024

Abstract The nematode Caenorhabditis elegans is an unconventional model in chronobiology, reported to exhibit physiological and behavioural circadian rhythms while lacking a defined transcriptional oscillator. extent importance of C. remain uncertain, given probable lack functional conservation key proteins, relatively non-robust ambiguous diel ecology. Here, we investigated the temporal coordination gene expression post-development using RNA sequencing. Over time series, which synchronised nematodes combined light temperature cycles, found clear evidence daily oscillations 343 genes JTK_Cycle. However, were not well-sustained constant conditions, with only 13 remaining significantly rhythmic. Reanalysis previous transcriptomic data echoed this finding identifying far fewer rhythmic also greater number overall. Weighted co-expression network analysis (WGCNA), hierarchical clustering approach, further confirmed prevalent environmentally driven RNA-seq data. This additionally revealed novel trend over 1000 exhibited hitherto unreported 16-hour oscillations, highlighting new facet .

Language: Английский

Citations

0