bims-ciryme 2025-01-26 papers

Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230483

Andrei Mihut, John S O'Neill, Carrie L Partch, Priya Crosby.

Daily rhythms in the activities of PERIOD proteins are critical to the temporal regulation of mammalian physiology. While the molecular partners and genetic circuits that allow PERIOD to effect auto-repression and regulate transcriptional programmes are increasingly well understood, comprehension of the time-resolved mechanisms that allow PERIOD to conduct this daily dance is incomplete. Here, we consider the character and controversies of this central mammalian clock protein with a focus on its intrinsically disordered nature.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Keywords: PERIOD/ PER; biomolecular condensation/ phase separation; cellular clock; circadian rhythm; intrinsically disordered regions (IDRs); post-translational modification

DOI: https://doi.org/10.1098/rstb.2023.0483

Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230346

Circadian gating: concepts, processes, and opportunities.

Pirita Paajanen, Jacqueline M Kimmey, Antony N Dodd.

Circadian clocks provide a biological measure of time that coordinates metabolism, physiology and behaviour with 24 h cycles in the environment. Circadian systems have a variety of characteristic properties, such as entrainment to environmental cues, a self-sustaining rhythm of about 24 h and temperature compensation of the circadian rhythm. In this perspective, we discuss the process of circadian gating, which refers to the restriction of a biological event to particular times of day by the circadian clock. We introduce principles and processes associated with circadian gating in a variety of organisms, including some associated mechanisms. We highlight socioeconomic opportunities presented by the investigation of circadian gating, using selected examples from circadian medicine and agricultural crop production to illustrate its importance.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Keywords: agriculture; chronobiology; chronotherapy; circadian gating; circadian rhythms

DOI: https://doi.org/10.1098/rstb.2023.0346

Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230473

Circadian metabolic adaptations to infections.

Claudio Costantini, Stefano Brancorsini, Francesco Grignani, Luigina Romani, Marina Maria Bellet.

Circadian clocks are biological oscillators that evolved to coordinate rhythms in behaviour and physiology around the 24-hour day. In mammalian tissues, circadian rhythms and metabolism are highly intertwined. The clock machinery controls rhythmic levels of circulating hormones and metabolites, as well as rate-limiting enzymes catalysing biosynthesis or degradation of macromolecules in metabolic tissues, such control being exerted both at the transcriptional and post-transcriptional level. During infections, major metabolic adaptation occurs in mammalian hosts, at the level of both the single immune cell and the whole organism. Under these circumstances, the rhythmic metabolic needs of the host intersect with those of two other players: the pathogen and the microbiota. These three components cooperate or compete to meet their own metabolic demands across the 24 hours. Here, we review findings describing the circadian regulation of the host response to infection, the circadian metabolic adaptations occurring during host-microbiota-pathogen interactions and how such regulation can influence the immune response of the host and, ultimately, its own survival.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Keywords: circadian clock; immune response; metabolism; microbiota; pathogen

DOI: https://doi.org/10.1098/rstb.2023.0473

BMC Genomics. 2025 Jan 21. 26(1): 56

Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types.

Prakash Basnet, Sevin Lee, Ka Hee Moon, Nam-Il Park, Gang-Seob Lee, Seongkon Lee, Taeyoung Um, Ik-Young Choi.

BACKGROUND: Plant senescence is the process of physiological maturation of plants and is important for crop yield and quality. Senescence is controlled by several factors, such as temperature and photoperiod. However, the molecular basis by which these genes promote senescence in soybeans is not well understood. We identified senescence-related genes via transcriptome analysis of early-senescence (ES)- and late-senescence (LS)-type plants to elucidate the molecular mechanisms of senescence in soybeans.
RESULTS: We obtained early-senescence (ES)- and late-senescence (LS)-type F7 plants from a cross between a hybrid (Glycine max × Glycine soja) and the Glycine max cultivar. The ES-type plants presented the reproductive (R2) growth stage at 50 days after sowing (DAS) and the R7 growth stage at 95 DAS, whereas the LS-type plants presented the beginning of the R1 and R6 growth stages at 50 and 95 DAS, respectively. To understand the molecular mechanisms underlying this senescence, we performed transcriptome analysis of leaves from 50 to 95 DAS of ES- and LS-type plants. A total of 2,414 and 2,471 genes at 50 and 95 DAS, respectively, were differentially expressed between ES-type and LS-type plants. Twenty-three candidate genes associated with the circadian clock, chlorophyll biosynthesis, phytohormones, and senescence-associated protein kinases were identified, and their expression levels were analyzed. In addition, to understand interaction between circadian clock and senescence, we analyzed expression patterns of seven circadian clock-related genes during the time period (light and dark condition): CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), CONSTANS-LIKE 9 (COL9), LUX ARRHYTHMO (LUX) EARLY FLOWERING 3 (ELF3), PSEUDO-RESPONSE REGULATOR5 (PRR5) and GIGANTEA (GI). The expression patterns of circadian clock-related genes were similar in the ES- and LS-type plants. However, the transcription levels of these genes were compared between ES- and LS-type plants, and the expression of these genes was greater than that in LS-type plants during the period when expression increased. Therefore, each set of candidate genes regulated senescence in each plant by regulating their expression level.
CONCLUSIONS: These findings provide novel insights into the regulation of senescence in soybean plants, which could lead to the development of new strategies to improve agriculture.

Keywords: Circadian clock; Inbred lines; Senescence; Soybean; Transcriptome analysis

DOI: https://doi.org/10.1186/s12864-024-11095-3

Philos Trans R Soc Lond B Biol Sci. 2025 Jan 23. 380(1918): 20230477

Circadian rhythms: pervasive, and often times evasive.

Luis F Larrondo.

Most circadian texts begin by stating that clocks are pervasive throughout the tree of life. Indeed, clock mechanisms have been described from cyanobacteria to humans, representing a notable example of convergent evolution: yet, there are several phyla in animals, protists or within fungi and bacteria, in which homologs of some-or all-known clock components seem to be absent, posing inevitable questions about the evolution of circadian systems. Moreover, as we move away from model organisms, there are several taxa in which core clock elements can be identified at the genomic levels. However, the functional description of those putative clocks has been hard to achieve, as rhythmicity is not observed unless defined abiotic or nutritional cues are provided. The mechanisms 'conditioning' the functionality of clocks remain uncertain, emphasizing the need to delve further into non-model circadian systems. As the absence of evidence is not evidence of absence, the lack of known core-clock homologs or of observable rhythms in a given organism, cannot be an a priori criterion to discard the presence of a functional clock, as rhythmicity may be limited to yet untested experimental conditions or phenotypes. This article seeks to reflect on these topics, highlighting some of the pressing questions awaiting to be addressed.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Keywords: TTFL; circadian rhythms; conditional rhythms; evolution; fungal clocks

DOI: https://doi.org/10.1098/rstb.2023.0477

Clin Epigenetics. 2025 Jan 22. 17(1): 12

Associations of maternal night shift work during pregnancy with DNA methylation in offspring: a meta-analysis in the PACE consortium.

BACKGROUND: Night shift work during pregnancy has been associated with differential DNA methylation in placental tissue, but no studies have explored this association in cord blood. We aimed to examine associations of maternal night shift work with cord blood DNA methylation.
METHODS: A total of 4487 mother-newborn pairs from 7 studies were included. Maternal night shift work during pregnancy was ascertained via questionnaires and harmonized into "any" versus "no". DNA methylation was measured in cord blood using the Illumina Infinium Methylation arrays. Robust linear regression models adjusted for relevant confounders were run in the individual cohorts, and results were meta-analyzed.
RESULTS: Maternal night shift work during pregnancy ranged from 3.4% to 26.3%. Three CpGs were differentially methylated in relation to maternal night shift work during pregnancy at a false discovery rate adjusted P < 0.05: cg10945885 (estimate (β) 0.38%, standard error (SE) 0.07), cg00773359 (β 0.25%, SE 0.05), and cg21836426 (β - 0.29%, SE 0.05). Associations of the identified CpGs were found in previous literature for gestational age and childhood and adolescent BMI. In a mouse model of prenatal jet lag exposure, information on offspring DNA methylation of ten homologous genes annotated to the 16 CpGs with P < 1 × 10-5 in our analysis was available, of which eight were associated (enrichment P: 1.62 × 10-11).
CONCLUSION: Maternal night shift work during pregnancy was associated with newborn DNA methylation at 3 CpGs. Top findings overlapped with those in a mouse model of gestational jet lag. This work strengthens evidence that DNA methylation could be a marker or mediator of impacts of circadian rhythm disturbances.

Keywords: Cohort study; DNA methylation; Epigenetics; Night shift work; Pregnancy

DOI: https://doi.org/10.1186/s13148-024-01810-y