Exercise and Gene Expression

The effects of exercise on epigenetic modifications: focus on DNA methylation, histone modifications and non-coding RNAs

Physical activity on a regular basis has been shown to bolster the overall wellness of an individual; research is now revealing that these changes are accompanied by epigenetic modifications. Regular exercise has been proven to make intervention plans more successful and prolong adherence to them. When it comes to epigenetic changes, there are four primary components. This includes changes to the DNA, histones, expression of particular non-coding RNAs and DNA methylation. External triggers, such as physical activity, can lead to modifications in the epigenetic components, resulting in changes in the transcription process. This report pays attention to the current knowledge that pertains to the epigenetic alterations that occur after exercise, the genes affected and the resulting characteristics.

The Impact of Physical Exercise on microRNAs in Hemodialysis Patients: A Review and a Protocol for an Ancillary Study

Physical inactivity is considered a significant risk factor for mortality and morbidity among chronic hemodialysis (HD) patients. Therefore, physical exercise is recommended in the treatment of HD patients. Although the beneficial effects of physical exercise in HD patients are well-described in the literature, the underlying physiological mechanisms still need to be fully understood. Recently, microRNAs (miRNAs) have emerged as potential mediators of the therapeutic effects of physical exercise in healthy individuals. miRNAs are short, single-stranded, noncoding RNAs involved in gene expression regulation. Specifically, upon forming the RNA-induced silencing complex, miRNAs selectively bind to specific miRNAs within cells, reducing gene expression. miRNAs can be secreted by cells in an accessible form or enclosed within exosomes or extracellular vesicles. They can be detected in various body fluids, including serum (circulating miRNAs), facilitating the study of their diverse expression. Currently, there is no available data regarding the impact of physical exercise on the expression of miRNAs involved in osteogenic differentiation, a fundamental mechanism in the development of vascular calcification, for HD patients. Therefore, we have designed an observational and longitudinal case-control study to evaluate the expression of miR-9 and miR-30b in HD patients participating in a 3-month interdialytic physical exercise program. This paper aims to present the study protocol and review the expression of circulating miRNAs in HD patients and their modulation through physical exercise.

International Society of Sports Nutrition Position Stand: Effects of essential amino acid supplementation on exercise and performance

Position Statement: The International Society of Sports Nutrition (ISSN) presents this position based on a critical examination of literature surrounding the effects of essential amino acid (EAA) supplementation on skeletal muscle maintenance and performance. This position stand is intended to provide a scientific foundation to athletes, dietitians, trainers, and other practitioners as to the benefits of supplemental EAA in both healthy and resistant (aging/clinical) populations. EAAs are crucial components of protein intake in humans, as the body cannot synthesize them. The daily recommended intake (DRI) for protein was established to prevent deficiencies due to inadequate EAA consumption. The following conclusions represent the official position of the Society: 1. Initial studies on EAAs' effects on skeletal muscle highlight their primary role in stimulating muscle protein synthesis (MPS) and turnover. Protein turnover is critical for replacing degraded or damaged muscle proteins, laying the metabolic foundation for enhanced functional performance. Consequently, research has shifted to examine the effects of EAA supplementation - with and without the benefits of exercise - on skeletal muscle maintenance and performance. 2. Supplementation with free-form EAAs leads to a quick rise in peripheral EAA concentrations, which in turn stimulates MPS. 3. The safe upper limit of EAA intake (amount), without inborn metabolic disease, can easily accommodate additional supplementation. 4. At rest, stimulation of MPS occurs at relatively small dosages (1.5-3.0 g) and seems to plateau at around 15-18 g. 5. The MPS stimulation by EAAs does not require non-essential amino acids. 6. Free-form EAA ingestion stimulates MPS more than an equivalent amount of intact protein. 7. Repeated EAA-induced MPS stimulation throughout the day does not diminish the anabolic effect of meal intake. 8. Although direct comparisons of various formulas have yet to be investigated, aging requires a greater proportion of leucine to overcome the reduced muscle sensitivity known as "anabolic resistance." 9. Without exercise, EAA supplementation can enhance functional outcomes in anabolic-resistant populations. 10. EAA requirements rise in the face of caloric deficits. During caloric deficit, it's essential to meet whole-body EAA requirements to preserve anabolic sensitivity in skeletal muscle.

Special Issue on Metabolic Adaptations in Cardiac and Skeletal Muscle during Acute and Chronic Exercise

Research in the field of exercise physiology has evolved dramatically over the last century [...].

The impact of metabolism on the adaptation of organisms to environmental change

Since Jacob and Monod's discovery of the lac operon ∼1960, the explanations offered for most metabolic adaptations have been genetic. The focus has been on the adaptive changes in gene expression that occur, which are often referred to as "metabolic reprogramming." The contributions metabolism makes to adaptation have been largely ignored. Here we point out that metabolic adaptations, including the associated changes in gene expression, are highly dependent on the metabolic state of an organism prior to the environmental change to which it is adapting, and on the plasticity of that state. In support of this hypothesis, we examine the paradigmatic example of a genetically driven adaptation, the adaptation of E. coli to growth on lactose, and the paradigmatic example of a metabolic driven adaptation, the Crabtree effect in yeast. Using a framework based on metabolic control analysis, we have reevaluated what is known about both adaptations, and conclude that knowledge of the metabolic properties of these organisms prior to environmental change is critical for understanding not only how they survive long enough to adapt, but also how the ensuing changes in gene expression occur, and their phenotypes post-adaptation. It would be useful if future explanations for metabolic adaptations acknowledged the contributions made to them by metabolism, and described the complex interplay between metabolic systems and genetic systems that make these adaptations possible.

Exe-Muscle: An Exercised Human Skeletal Muscle Gene Expression Database

Human muscle tissue undergoes dynamic changes in gene expression during exercise, and the dynamics of these genes are correlated with muscle adaptation to exercise. A database of gene expression changes in human muscle before and after exercise was established for data mining. A web-based searchable database, Exe-muscle, was developed using microarray sequencing data, which can help users to retrieve gene expression at different times. Search results provide a complete description of target genes or genes with specific expression patterns. We can explore the molecular mechanisms behind exercise science by studying the changes in muscle gene expression over time before and after exercise. Based on the high-throughput microarray data before and after human exercise, a human pre- and post-exercise database was created using web-based database technology, which researchers can use or share their gene expression data. The Exe-muscle database is accessible online.

Can Exercise Training Alter Human Skeletal Muscle DNA Methylation?

Skeletal muscle is highly plastic and dynamically regulated by the body’s physical demands. This study aimed to determine the plasticity of skeletal muscle DNA methylation in response to 8 weeks of supervised exercise training in volunteers with a range of insulin sensitivities. We studied 13 sedentary participants and performed euglycemic hyperinsulinemic clamps with basal vastus lateralis muscle biopsies and peak aerobic activity (VO2 peak) tests before and after training. We extracted DNA from the muscle biopsies and performed global methylation using Illumina’s Methylation EPIC 850K BeadChip. Training significantly increased peak aerobic capacity and insulin-stimulated glucose disposal. Fasting serum insulin and insulin levels during the steady state of the clamp were significantly lower post-training. Insulin clearance rates during the clamp increased following the training. We identified 13 increased and 90 decreased differentially methylated cytosines (DMCs) in response to 8 weeks of training. Of the 13 increased DMCs, 2 were within the following genes, FSTL3, and RP11-624M8.1. Of the 90 decreased DMCs, 9 were within the genes CNGA1, FCGR2A, KIF21A, MEIS1, NT5DC1, OR4D1, PRPF4B, SLC26A7, and ZNF280C. Moreover, pathway analysis showed an enrichment in metabolic and actin-cytoskeleton pathways for the decreased DMCs, and for the increased DMCs, an enrichment in signal-dependent regulation of myogenesis, NOTCH2 activation and transmission, and SMAD2/3: SMAD4 transcriptional activity pathways. Our findings showed that 8 weeks of exercise training alters skeletal muscle DNA methylation of specific genes and pathways in people with varying degrees of insulin sensitivity.

Plasma microRNA-320a as a Potential Biomarker of Physiological Changes during Training in Professional Volleyball Players

A deeper insight into the mechanisms responsible for athlete performance that may serve as specific and detailed training indicators is still desired, because conventionally used biomarkers provide limited information about the adaptive processes that occur during exercise. The objective of our study was to assess insulin-like growth factor 1 receptors (IGF1R) gene expression and evaluate plasma concentration of selected microRNAs (miRNAs) during a 10-week training period (sampling times: week 1, 4, 7, and 10) in a group of 12 professional female volleyball players. Circulating miRNAs (miR-223, miR-320a, and miR-486) with established concentration in plasma and documented association with the IGF1 signaling pathway, which is involved in muscle development and recovery, were tested. The levels of analyzed miRNAs, tested by one-way ANOVA, were significantly different between four training periods during a 10-week training cycle (miR-223 p < 0.0001, miR-320a p = 0.00021, miR-486 p = 0.0037, respectively). The levels of IGF1R also appeared to be different (p = 0.00092), and their expression showed a trend to increase between the first and third periods. In the fourth period, the expression decreased, although it was higher compared with the baseline. Correlations between concentration levels of miR-223 and miR-320a (rs = 0.54, p < 0.001), as well as between miR-320a and miR-486 (rs = 0.73, p < 0.001) were also found. In the fourth period, a negative correlation between miR-223 plasma level and leucocyte IGF1R expression was found (rs = -0.63, p = 0.028). Multiple linear regression analysis showed that miR-320a (p = 0.024) and creatine kinase (p = 0.028) had the greatest impact on the expression levels of the IGF1R gene. Future studies are required to define whether these miRNAs, especially miR-320a, as well as IGF1R expression could be useful biomarkers of physiological changes during exercise and to discover their detailed biological roles in mode-specific exercise training adaptations of professional athletes.

Potential Physiological and Cellular Mechanisms of Exercise That Decrease the Risk of Severe Complications and Mortality Following SARS-CoV-2 Infection

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has unmasked mankind's vulnerability to biological threats. Although higher age is a major risk factor for disease severity in COVID-19, several predisposing risk factors for mortality are related to low cardiorespiratory and metabolic fitness, including obesity, cardiovascular disease, diabetes, and hypertension. Reaching physical activity (PA) guideline goals contribute to protect against numerous immune and inflammatory disorders, in addition to multi-morbidities and mortality. Elevated levels of cardiorespiratory fitness, being non-obese, and regular PA improves immunological function, mitigating sustained low-grade systemic inflammation and age-related deterioration of the immune system, or immunosenescence. Regular PA and being non-obese also improve the antibody response to vaccination. In this review, we highlight potential physiological, cellular, and molecular mechanisms that are affected by regular PA, increase the host antiviral defense, and may determine the course and outcome of COVID-19. Not only are the immune system and regular PA in relation to COVID-19 discussed, but also the cardiovascular, respiratory, renal, and hormonal systems, as well as skeletal muscle, epigenetics, and mitochondrial function.

Maternal physical activity significantly alters the placental transcriptome

INTRODUCTION

Maternal lifestyle, in particular physical activity (PA), influences many of the physiological adaptations during pregnancy associated with feto-placental development and growth. There is limited to no information on the link between PA during pregnancy and the molecular mechanisms governing placental function. The aim of this study was to investigate the molecular mechanisms through which maternal PA may influence placental function.

METHODS

The level of PA was measured by accelerometry and gene expression was measured in term placenta with custom polymerase chain reaction (PCR) arrays and microarray analysis followed by a pathway analyses on significantly differentially expressed genes (DEGs).

RESULTS

Microarray analysis showed 43 significantly DEGs between active and non-active participants. RT-qPCR validation of a sub-sample of DEGs revealed significant changes in the level of expression between active and non-active moms (student's t-test, p < 0.05, n = 11). Genes involved in transport of water (p = 0.00236) and uptake of glycerol (p = 0.00219) were enriched in active moms. PA was also associated with the alteration of alternative splicing patters. The most consistent splicing changes were observed for AQP9 where active moms lacked exon 2.

DISCUSSION

Variations in maternal PA influences placental gene. We show significant expression changes of genes that are involved in transport and localization between active and non-active women. Most notably, the expression of the aquaporin family of genes (e.g. AQP1 and AQP9) were found to be significantly higher in the placentas of active women suggesting an adaptive response for the transport of water and glycerol in this population.

The Prospective Study of Epigenetic Regulatory Profiles in Sport and Exercise Monitored Through Chromosome Conformation Signatures

The integration of genetic and environmental factors that regulate the gene expression patterns associated with exercise adaptation is mediated by epigenetic mechanisms. The organisation of the human genome within three-dimensional space, known as chromosome conformation, has recently been shown as a dynamic epigenetic regulator of gene expression, facilitating the interaction of distal genomic regions due to tight and regulated packaging of chromosomes in the cell nucleus. Technological advances in the study of chromosome conformation mean a new class of biomarker-the chromosome conformation signature (CCS)-can identify chromosomal interactions across several genomic loci as a collective marker of an epigenomic state. Investigative use of CCSs in biological and medical research shows promise in identifying the likelihood that a disease state is present or absent, as well as an ability to prospectively stratify individuals according to their likely response to medical intervention. The association of CCSs with gene expression patterns suggests that there are likely to be CCSs that respond, or regulate the response, to exercise and related stimuli. The present review provides a contextual background to CCS research and a theoretical framework discussing the potential uses of this novel epigenomic biomarker within sport and exercise science and medicine.

Genetic Networks Underlying Natural Variation in Basal and Induced Activity Levels in Drosophila melanogaster

Exercise is recommended by health professionals across the globe as part of a healthy lifestyle to prevent and/or treat the consequences of obesity. While overall, the health benefits of exercise and an active lifestyle are well understood, very little is known about how genetics impacts an individual's inclination for and response to exercise. To address this knowledge gap, we investigated the genetic architecture underlying natural variation in activity levels in the model system Drosophila melanogaster Activity levels were assayed in the Drosophila Genetics Reference Panel fly strains at baseline and in response to a gentle exercise treatment using the Rotational Exercise Quantification System. We found significant, sex-dependent variation in both activity measures and identified over 100 genes that contribute to basal and induced exercise activity levels. This gene set was enriched for genes with functions in the central nervous system and in neuromuscular junctions and included several candidate genes with known activity phenotypes such as flightlessness or uncoordinated movement. Interestingly, there were also several chromatin proteins among the candidate genes, two of which were validated and shown to impact activity levels. Thus, the study described here reveals the complex genetic architecture controlling basal and exercise-induced activity levels in D. melanogaster and provides a resource for exercise biologists.

The iReAct study - A biopsychosocial analysis of the individual response to physical activity

Background

Physical activity is a substantial promoter for health and well-being. Yet, while an increasing number of studies shows that the responsiveness to physical activity is highly individual, most studies focus this issue from only one perspective and neglect other contributing aspects. In reference to a biopsychosocial framework, the goal of our study is to examine how physically inactive individuals respond to two distinct standardized endurance trainings on various levels. Based on an assessment of activity- and health-related biographical experiences across the life course, our mixed-method study analyzes the responsiveness to physical activity in the form of a transdisciplinary approach, considering physiological, epigenetic, motivational, affective, and body image-related aspects.

Methods

Participants are randomly assigned to two different training programs (High Intensity Interval Training vs. Moderate Intensity Continuous Training) for six weeks. After this first training period, participants switch training modes according to a two-period sequential-training-intervention (STI) design and train for another six weeks. In order to analyse baseline characteristics as well as acute and adaptive biopsychosocial responses, three extensive mixed-methods diagnostic blocks take place at the beginning (t₀) of the study and after the first (t₁) and the second (t₂) training period resulting in a net follow-up time of 15 weeks. The study is divided into five modules in order to cover a wide array of perspectives.

Discussion

The study's transdisciplinary mixed-method design allows to interlace a multitude of subjective and objective data and therefore to draw an integrated picture of the biopsychosocial efficacy of two distinct physical activity programs. The results of our study can be expected to contribute to the development and design of individualised training programs for the promotion of physical activity.

Trial registration

The study was retrospectively registered in the German Clinical Trials Register on 12 June 2019 (DRKS00017446).

Epigenetic changes in healthy human skeletal muscle following exercise- a systematic review

Exercise training is continually challenging whole-body homeostasis, leading to improvements in performance and health. Adaptations to exercise training are complex and are influenced by both environmental and genetic factors. Epigenetic factors regulate gene expression in a tissue-specific manner and constitute a link between the genotype and the environment. Moreover, epigenetic factors are emerging as potential biomarkers that could predict the response to exercise training. This systematic review aimed to identify epigenetic changes that have been reported in skeletal muscle following exercise training in healthy populations. A literature search of five databases (PUBMED, MEDLINE, CINHAL, SCOPUS and SportDiscuss) was conducted in November 2018. Articles were included if they examined epigenetic modifications (DNA methylation, histone modifications and non-coding RNAs) in skeletal muscle, following either an acute bout of exercise, an exercise intervention in a pre/post design, or a case/control type of study. Twenty-two studies met the inclusion criteria. Several epigenetic markers including DNA methylation of genes known to be differentially expressed after exercise and myomiRs were reported to be modified after exercise. Several epigenetic marks were identified to be altered in response to exercise, with potential influence on skeletal muscle metabolism. However, whether these epigenetic marks play a role in the physiological impact of exercise is unclear. Exercise epigenetics is still a very young research field, and it is expected that in the future the causality of such changes will be elucidated via the utilization of emerging experimental models able to target the epigenome.

Genetic and epigenetic sex-specific adaptations to endurance exercise

In recent years, the interest in personalised interventions such as medicine, nutrition, and exercise is rapidly rising to maximize health outcomes and ensure the most appropriate treatments. Exercising regularly is recommended for both healthy and diseased populations to improve health. However, there are sex-specific adaptations to exercise that often are not taken into consideration. While endurance exercise training alters the human skeletal muscle epigenome and subsequent gene expression, it is still unknown whether it does so differently in men and women, potentially leading to sex-specific physiological adaptations. Elucidating sex differences in genetics, epigenetics, gene regulation and expression in response to exercise will have great health implications, as it may enable gene targets in future clinical interventions and may better individualised interventions. This review will cover this topic and highlight the recent findings of sex-specific genetic, epigenetic, and gene expression studies, address the gaps in the field, and offer recommendations for future research.

Hepatic gene expression in mouse models of non-alcoholic fatty liver disease after acute exercise

AIM

Non-alcoholic fatty liver disease (NAFLD) patients benefit from physical exercise. This study aimed to investigate the effect of acute exercise on hepatic gene expression in different mouse models of NAFLD.

METHODS

C57BL/6J mice were fed with a control (CD) or a high fat (HFD) diet. AlbCrePten^flox/flox (Pten-KO) and Fxr^-/- mice, two genetic models of NAFLD with insulin hypersensitivity and resistance, respectively, were fed with CD. After 4 weeks, mice were randomly assigned to exercise or sedentariness. Mice were killed 15 min or 3 h after the running/sedentary period. Genome-wide hepatic gene expression was evaluated with the Illumina Micro-array platform. Quantitative polymerase chain reaction confirmed changes in gene expression.

RESULTS

Acute exercise transiently affected the expression of genes involved in the immune response in C57BL/6 mice fed with CD and this effect normalized in the recovery phase. Acute exercise affected genes involved in gluconeogenesis in the insulin resistant Fxr^-/- model. Genes involved in lipid metabolism were affected in C57BL/6 mice fed with CD, but not in mouse models of NAFLD. Genes involved in DNA damage response pathways were deregulated only in C57BL/6 mice fed with CD and not in mouse models of NAFLD.

CONCLUSION

The simultaneous analysis of different NAFLD models revealed that an acute exercise bout affects hepatic gene expression differentially according to animal models and that most of the differentially expressed genes are involved in glucose and fatty acid metabolism, immune regulation, and DNA damage response.

Energy Constraint as a Novel Mechanism Linking Exercise and Health

Humans and other species adapt dynamically to changes in daily physical activity, maintaining total energy expenditure within a narrow range. Chronic exercise thus suppresses other physiological activity, including immunity, reproduction, and stress response. This exercise-induced downregulation improves health at moderate levels of physical activity but can be detrimental at extreme workloads.

Exercise Training and Epigenetic Regulation: Multilevel Modification and Regulation of Gene Expression

Exercise training elicits acute and adaptive long term changes in human physiology that mediate the improvement of performance and health state. The responses are integrative and orchestrated by several mechanisms, as gene expression. Gene expression is essential to construct the adaptation of the biological system to exercise training, since there are molecular processes mediating oxidative and non-oxidative metabolism, angiogenesis, cardiac and skeletal myofiber hypertrophy, and other processes that leads to a greater physiological status. Epigenetic is the field that studies about gene expression changes heritable by meiosis and mitosis, by changes in chromatin and DNA conformation, but not in DNA sequence, that studies the regulation on gene expression that is independent of genotype. The field approaches mechanisms of DNA and chromatin conformational changes that inhibit or increase gene expression and determine tissue specific pattern. The three major studied epigenetic mechanisms are DNA methylation, Histone modification, and regulation of noncoding RNA-associated genes. This review elucidates these mechanisms, focusing on the relationship between them and their relationship with exercise training, physical performance and the enhancement of health status. On this chapter, we clarified the relationship of epigenetic modulations and their intimal relationship with acute and chronic effect of exercise training, concentrating our effort on skeletal muscle, heart and vascular responses, that are the most responsive systems against to exercise training and play crucial role on physical performance and improvement of health state.