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Nucleus Type-Specific DNA Methylomics Reveals Epigenetic “Memory” of Prior Adaptation in Skeletal Muscle

ABSTRACT: Using a mouse model of conditional and inducible in vivo fluorescent myonuclear labeling (HSA-GFP), sorting purification of nuclei, low-input reduced representation bisulfite sequencing (RRBS), and a translatable and reversible model of exercise (progressive weighted wheel running, PoWeR), we provide the first nucleus type-specific epigenetic information on skeletal muscle adaptation and detraining along with whole muscle transcriptomics.

ORGANISM(S): Mus musculus

PROVIDER: GSE180877 | GEO | 2021/12/08

REPOSITORIES: GEO

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Nucleus Type-Specific DNA Methylomics Reveals Epigenetic "Memory" of Prior Adaptation in Skeletal Muscle

Project description:Using a mouse model of conditional and inducible in vivo fluorescent myonuclear labeling (HSA-GFP), sorting purification of nuclei, low-input reduced representation bisulfite sequencing (RRBS), and a translatable and reversible model of exercise (progressive weighted wheel running, PoWeR), we provide the first nucleus type-specific epigenetic information on skeletal muscle adaptation and detraining.

2021-12-08 | GSE180433 | GEO

Effect of wheel running exercise on gene expression in skeletal muscles of mice

Project description:This analysis was done to determine which muscle group has the most skeletal muscle transcriptional reponses to wheel running activity. Seven male mice with C57BL/6 genetic background were placed individually in cages with running wheels and allowed free access to the wheels 24 hr per day. Access to running wheels began when the mice were 6 months old, and continued for 12 weeks. The morning after the night of running, the mice were euthanized and several muscle groups were snap froze in liquid nitrogen to preserve RNA. The same muscle groups were collected from three age-matched "sedentary" mice that were housed in ordinary cages that did not permit sustained running. For each muscle group, separate pools of polyadenylated RNA from the sedentary and wheel-running mice were prepared for deep sequencing of cDNA with the SOLiD 3 platform. Four muscle groups were examined (quadriceps femoris; gastrocnemius/plantaris; tibialis anterior; triceps brachii). For each muscle, RNA was pooled from 3 sedentary or 7 wheel-running mice (8 pools total).

2011-09-03 | E-GEOD-31843 | biostudies-arrayexpress

Effect of wheel running exercise on gene expression in skeletal muscles of mice

2011-09-03 | GSE31843 | GEO

PolyA RNA sequencing of soleus muscles of WT and LSD1-mKO mice after voluntary wheel running

Project description:To understand the role of LSD1 in transcriptional regulation in muscle under voluntary wheel running (VWR) training, RNA-seq analyses of soleus muscles of skeletal muscle-specific LSD1 KO mice (LSD1-mKO mice) and WT mice after VWR were carried out. We found that loss of LSD1 led to increased expression of oxidative metabolism genes in soleus muscle.

2023-01-24 | GSE198827 | GEO

Proteome profiles of skeletal muscle connective tissue: Influence of aging and physical training

Project description:Both aging and physical activity can influence the amount of connective tissue in skeletal muscle, but the impact of these upon specific extracellular matrix (ECM) proteins in skeletal muscle is unknown. We investigated the proteome profile of connective tissue in skeletal muscle by label-free proteomic analysis of on cellular protein-depleted extracts from lateral gastrocnemius muscle of old (22-23 months old) and middle-aged mice (11 months old) subjected to three different levels of regular physical activity for 10 weeks (high resistance wheel running, low resistance wheel running or sedentary controls). We hypothesized that aging is correlated with increased amount of connective tissue proteins in skeletal muscle, and that regular physical activity can counteract these age-related changes. We found that dominating cellular proteins were diminished in the urea/thiourea extract, which was therefore used for proteomics. Proteomic analysis identified 482 proteins and showed enrichment for ECM proteins. Statistical analysis revealed that the abundances of 86 proteins were changed with age. Twenty-three of these differentially abundant proteins were identified as structural ECM proteins (e.g., collagens and laminins) and all of these were significantly more abundant with aging. No significant effect of training or interaction between training and advance in age was found for any proteins. Finally, we found a lower protein concentration in the urea/thiourea extracts from the old compared to middle-aged mice. These findings indicate that intramuscular connective tissue alters its protein content with age but is unaffected by training.

2023-04-27 | PXD036532 | Pride

RNA-sequencing in skeletal muscle from a mouse model of laparotomy with pre-operative running wheel exercise

Project description:This study aimed to characterize the effects of pre-operative volitional running wheel exercise on post-operative physical function and skeletal muscle gene expression in 24-month-old C57BL/6N mice following laparotomy. Soleus muscles collected on post-operative day 5 (POD 5) were used for this study.

2022-04-28 | GSE201252 | GEO

Aerobic Exercise Improves Molecular and Functional Deficits in A Murine Model of Facioscapulohumeral Muscular Dystrophy

Project description:We investigated the effects of six weeks of voluntary wheel running in heterozygous B6(Cg)-Gt(ROSA)26Sortm1.1(DUX4*)Plj/J (FLExDUX4) mouse model of Facioscapulohumeral Muscular Dystrophy (FSHD) and their wild type (WT) littermates to characterize the structural/functional adaptations to voluntary wheel running and their molecular foundations using RNA sequencing

2023-12-01 | GSE233340 | GEO

Effects of wheel running exercise and myostatin depletion on skeletal muscle gene expression in mice

Project description:This SuperSeries is composed of the following subset Series: GSE31839: Effect of wheel running exercise and myostatin depletion on gene expression in triceps brachii muscles of mice GSE31843: Effect of wheel running exercise on gene expression in skeletal muscles of mice Refer to individual Series

2011-09-02 | E-GEOD-31844 | biostudies-arrayexpress

Gene expression profiling of gastrocnemius of mini muscle mice

Project description:Few studies have investigated heterogeneity of selection response in replicate lines subjected to equivalent selection. We developed 4 replicate lines of mice based on high levels of voluntary wheel running (high runner or HR lines) while also maintaining 4 non-selected control lines. This led to the unexpected discovery of the HR mini-muscle (HRmini) phenotype, recognized by a 50% reduction in hindlimb muscle mass, which became fixed in 1 of the 4 HR selected lines. Here, we report genome-wide expression profiling describing transcriptome differences between HRnormal and HRmini medial gastrocnemius. This work provides a resource for understanding differences in muscle phenotypes in populations exhibiting high running capacity.

2013-02-19 | GSE41910 | GEO

RNA-seq of triceps brachii muscles from mice after myostatin depletion and wheel running exercise

Project description:The purpose of this study was to determine whether postdevelopmental myostatin depletion influenced the changes in skeletal muscle gene expression profiles induced by a long-term increase in physical activity. Myostatin levels in muscles of adult male mice with floxed myostatin genes were reduced ~85% by activating Cre recombinase. Control mice with normal myostatin genes had the same Cre-activating treatment. Some of the mice were housed in ordinary cages throughout the study, limiting their physical activity. Other mice were given free access to running wheels for the final 12 weeks of the study. At the end of the study, comprehensive gene expression profiles of triceps brachii muscles were determined by RNA sequencing (RNA-Seq), with muscles from mice selected for similarity of running behavior throughout the period of wheel access. Wheel running increased expression of hundreds of mRNAs encoding proteins involved in oxidative energy metabolism, and this response was not affected by myostatin deficiency. The running-induced increase in the ratio of Myh1 mRNA (which encodes myosin heavy chain type 2x) to Myh4 mRNA (which encodes myosin heavy chain type 2b) also was not affected by myostatin depletion. At every threshold of P (computed by analysis of variance), the number of transcripts with interactions between activity level and myostatin level was fewer than the number expected by chance. These data suggest that myostatin is not required for transcriptional adaptations to moderate-intensity exercise. 12 samples, 6 from sedentary mice and 6 from active (wheel running) mice. 3 control and 3 myostatin-deficient mice within each activity level.

2011-09-02 | E-GEOD-31839 | biostudies-arrayexpress

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