Day-night and seasonal variation of human gene expression across tissues.
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ABSTRACT:
SUBMITTER: Wucher V
PROVIDER: S-EPMC7941615 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways, and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions. This atlas may have multiple applications; for example, drug targets with day-night or seasonal variation in gene expression may benefit from temporally adjusted doses.
| S-EPMC9934459 | biostudies-literature
Project description:BackgroundDay-night behavioral variation is observed in most organisms, and is generally controlled by circadian clocks and/or synchronization to environmental cues. Hydra species, which are freshwater cnidarians, are thought to lack the core clock genes that form transcription-translation feedback loops in clock systems. In this study, we examined whether hydras exhibit diel rhythms in terms of behavior and gene expression levels without typical clock genes.ResultsWe found that the total behavior of hydras was elevated during the day and decreased at night under a 12-h light-dark cycle. Polyp contraction frequency, one component of behavior, exhibited a clear diel rhythm. However, neither total behavior nor polyp contraction frequency showed rhythmic changes under constant light and constant dark conditions. To identify the genes underlying diel behavior, we performed genome-wide transcriptome analysis of hydras under light-dark cycles. Using three different analytic algorithms, we found that 380 genes showed robust diel oscillations in expression. Some of these genes shared common features with diel cycle genes of other cnidarian species with endogenous clock systems.ConclusionHydras show diel behavioral rhythms under light-dark cycles despite the absence of canonical core clock genes. Given the functions of the genes showing diel oscillations in hydras and the similarities of those genes with the diel cycle genes of other cnidarian species with circadian clocks, it is possible that diel cycle genes play an important role across cnidarian species regardless of the presence or absence of core clock genes under light-dark cycles.
| S-EPMC6407280 | biostudies-literature
Project description:Background The aim of this study was to investigate the association between night-to-night adherence to continuous positive airway pressure (CPAP) therapy and both home blood pressure (BP) level on the following day and seasonal variation in home BP in patients with obstructive sleep apnea. Methods and Results We analyzed 105 participants who had been diagnosed with obstructive sleep apnea (average apnea-hypopnea index, 49.7±18.4 per hour) and who were already receiving CPAP therapy. Home BP (twice every morning and evening) and CPAP adherence data were automatically transmitted to a server for 1 year. A mixed-effects model for repeated measures analysis was used to examine associations of night-to-night good CPAP adherence with day-to-day home BP within the same patient after adjusting for covariates. The average number of days in which patients achieved both CPAP adherence and morning or evening home BP measurement was 206.6±122.7 days (21 487 readings) and 191.2±126.3 days (20 170 readings), respectively. Good CPAP adherence (>4 hours per night of use) was achieved on the evening or morning before home BP measurements (86.8% and 86.9%, respectively). After adjustment for confounders, good CPAP adherence was negatively associated with morning home systolic BP (β, -0.663; P=0.004) and diastolic BP (β, -0.829; P<0.001). Morning home systolic BP in winter in the individuals with good CPAP adherence was significantly lower than that in individuals without such adherence (P<0.05). These associations were not found in evening home BP. Conclusions Good adherence to CPAP therapy was negatively associated with morning home BP on the following day in patients with obstructive sleep apnea. The association was remarkable in the winter season.
| S-EPMC9075445 | biostudies-literature
Project description:IntroductionSleep disturbances are commonly reported in people living with Alzheimer's disease (AD), but it is currently unknown whether night-to-night variation in sleep predicts day-to-day variation in vigilance, cognition, mood, and behavior (daytime measures).MethodsSubjective and objective sleep and daytime measures were collected daily for 2 weeks in 15 participants with mild AD, eight participants with mild cognitive impairment (MCI), and 22 participants with no cognitive impairment (NCI). Associations between daytime measures and four principal components of sleep (duration, quality, continuity, and latency) were quantified using mixed-model regression.ResultsSleepiness, alertness, contentedness, everyday memory errors, serial subtraction, and behavioral problems were predicted by at least one of the components of sleep, and in particular sleep duration and continuity. Associations between variations in sleep and daytime measures were linear or quadratic and often different between participants with AD and those with NCI.DiscussionThese findings imply that daytime functioning in people with AD may be improved by interventions that target sleep continuity.
| S-EPMC9109375 | biostudies-literature
Project description:Circadian information is maintained in mammalian tissues by a cell-autonomous network of transcriptional feedback loops that have evolved to optimally regulate tissue-specific functions. An analysis of daily gene expression in different tissues, as well as an evaluation of inter-tissue circadian variability, is crucial for a systems-level understanding of this transcriptional circuitry. Affymetrix gene chip measurements of liver, muscle, adipose, and lung tissues were obtained from a rich time series light/dark experiment, involving 54 normal rats sacrificed at 18 time points within the 24-hr cycle. Our analysis revealed a high degree of circadian regulation with a variable distribution of phases among the four tissues. Interestingly, only a small number of common genes maintain circadian activity in all tissues, with many of them consisting of "core-clock" components with synchronous rhythms. Our results suggest that inter-tissue circadian variability is a critical component of homeostatic body function and is mediated by diverse signaling pathways that ultimately lead to highly tissue-specific transcription regulation.
| S-EPMC5945012 | biostudies-literature
Project description:Emu (Dromaius novaehollandiae) farming has been gaining wide interest for fat production. Oil rendered from this large flightless bird's fat is valued for its anti-inflammatory and antioxidant properties for uses in therapeutics and cosmetics. We analyzed the seasonal and sex-dependent differentially expressed (DE) genes involved in fat metabolism in emus. Samples were taken from back and abdominal fat tissues of a single set of four male and four female emus in April, June, and November for RNA-sequencing. We found 100 DE genes (47 seasonally in males; 34 seasonally in females; 19 between sexes). Seasonally DE genes with significant difference between the sexes in gene ontology terms suggested integrin beta chain-2 (ITGB2) influences fat changes, in concordance with earlier studies. Six seasonally DE genes functioned in more than two enriched pathways (two female: angiopoietin-like 4 (ANGPTL4) and lipoprotein lipase (LPL); four male: lumican (LUM), osteoglycin (OGN), aldolase B (ALDOB), and solute carrier family 37 member 2 (SLC37A2)). Two sexually DE genes, follicle stimulating hormone receptor (FSHR) and perilipin 2 (PLIN2), had functional investigations supporting their influence on fat gain and loss. The results suggested these nine genes influence fat metabolism and deposition in emus.
| S-EPMC9177602 | biostudies-literature
Project description:Differential allelic expression has been shown to be common in mice, humans and maize, and variability in the expression of polymorphic alleles has been associated with human disease. Here, we describe the differential expression pattern of Paraoxonase-1, a gene involved in lipid metabolism and implicated in the formation of atherosclerotic lesions. We measured the expression of the murine Paraoxonase-1 gene (Pon1) in livers at different stages of embryonic development using F1 hybrid crosses and quantified the transcriptional level of both parental alleles. Using human foetal tissues, we analysed the expression of the human orthologue (PON1) and found monoallelic or preferential allelic expression in 6/7 and 4/4 samples from liver and pancreas, respectively. We observed that Pon1 does not show a parent-of-origin preference in its allelic expression, but has dramatic variations in allele-specific expression occurring throughout development. This study has important repercussions in the analysis of haplotypes at disease loci, since it implies that the expression of polymorphic alleles can be unequal and dynamic.
| S-EPMC2566522 | biostudies-literature
Project description:PoolSeq analysis of seasonal variation in a natural population of the non-biting midge Chironomus riparius
| PRJEB35534 | ENA
Project description:Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge. Rare non-coding variants have been associated with extreme gene expression in studies using single tissues, but their effects across tissues are unknown. Here we identify gene expression outliers, or individuals showing extreme expression levels for a particular gene, across 44 human tissues by using combined analyses of whole genomes and multi-tissue RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project v6p release. We find that 58% of underexpression and 28% of overexpression outliers have nearby conserved rare variants compared to 8% of non-outliers. Additionally, we developed RIVER (RNA-informed variant effect on regulation), a Bayesian statistical model that incorporates expression data to predict a regulatory effect for rare variants with higher accuracy than models using genomic annotations alone. Overall, we demonstrate that rare variants contribute to large gene expression changes across tissues and provide an integrative method for interpretation of rare variants in individual genomes.
| S-EPMC5877409 | biostudies-literature
Project description:PurposeIt is known that delivery rates from spontaneous conception vary according to season which may be due to cultural or environmental factors; however, conflicting data exist regarding whether outcomes from IVF are also seasonally dependent. The present study was designed to test the hypothesis that the season at oocyte retrieval is associated with livebirth after fresh transfer.MethodsDates of oocyte retrieval for all autologous cycles in our IVF program between January 2012 and December 2017 were categorized by season. Dates were linked to local temperature (min, max, average) and day length obtained from meteorological records. Average maximum temperature and day length were categorized into tertiles. Multivariable logistic regression, adjusted for age and quadratic age, were used to model odds (aOR) of implantation, clinical pregnancy, spontaneous abortion, and livebirth.ResultsPatient characteristics were similar across seasons. As expected, temperature and day length varied by season. When compared with cycles started during winter, there was no difference in the age-adjusted odds of livebirth for the other three seasons (spring: aOR: 0.97, 95% CI: 0.82-1.13; summer: aOR: 1.05, 0.90-1.23; fall: aOR: 0.98, 0.84-1.15). There was a positive linear trend between temperature and odds of implantation, and clinical pregnancy (p value, test for linear trend (implantation, p = 0.02; clinical pregnancy, p = 0.01)) but no association with livebirth for temperature or day length.ConclusionsWe found that season at oocyte retrieval was not associated with livebirth, contrary to patterns seen in naturally conceived populations. However, our data did suggest modestly higher odds of clinical pregnancy for retrievals in June and July, and that higher temperature at time of retrieval was associated with higher odds of clinical pregnancy but not livebirth.
| S-EPMC7550498 | biostudies-literature