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The Myonuclear DNA Methylome in Response to an Acute Hypertrophic Stimulus

ABSTRACT: The Myonuclear DNA Methylome in Response to an Acute Hypertrophic Stimulus

PROVIDER: PRJNA604819 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11018409_1.fastq.gz	Fastqsanger.gz
	SRR11018409_2.fastq.gz	Fastqsanger.gz
	SRR11018410_1.fastq.gz	Fastqsanger.gz
	SRR11018410_2.fastq.gz	Fastqsanger.gz
	SRR11018411_1.fastq.gz	Fastqsanger.gz

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The Age-Dependent Resident Myonuclear Multi-Omic Response to an Acute Skeletal Muscle Hypertrophic Stimulus in Mice

Project description:A detailed analysis of how muscle fiber nuclei (myonuclei) respond to a hypertrophic stimulus would provide a critical step toward understanding compromised skeletal muscle plasticity with age. We used recombination-independent doxycycline-inducible myonucleus-specific fluorescent labelling, tissue RNA-sequencing, myonuclear DNA methylation analysis, multi-omic integration, and single myonucleus RNA-sequencing to define the molecular characteristics of adult (6-8 month) and aged (24 month) murine skeletal muscle after acute mechanical overload (MOV). In adult and aged MOV muscles, we found that: 1) similarities in the transcriptional response to loading – specifically in metabolism genes – were partly explained by a post-transcriptional microRNA-mediated mechanism, which we corroborated using an inducible muscle fiber-specific miR-1 knockout model, 2) differences in age-dependent transcriptional responses were linked to the magnitude and location of differential DNA methylation in resident myonuclei, specifically around hypertrophy-associated genes such as Myc, Runx1, Mybph, Ankrd1, collagen genes, and minichromosome maintenance genes, 3) adult and aged resident myonuclear transcriptomes had differing enrichment for innervation-related transcripts as well as unique transcriptional profiles in an Atf3+ “sarcomere assembly” population after MOV, and 4) cellular deconvolution analysis supports a role for neuromuscular junction regulation in age-specific hypertrophic adaptation. These data are a roadmap for uncovering molecular targets to enhance aged muscle adaptability.

2026-02-12 | GSE319289 | GEO

The Age-Dependent Resident Myonuclear Multi-Omic Response to an Acute Skeletal Muscle Hypertrophic Stimulus in Mice

Project description:The Age-Dependent Resident Myonuclear Multi-Omic Response to an Acute Skeletal Muscle Hypertrophic Stimulus in Mice

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The myonuclear DNA methylome in response to an acute hypertrophic stimulus.

Project description:In addition to multi-nucleated muscle fibres, numerous resident and infiltrating mononuclear cells populate the muscle compartment. As most epigenetic assays in skeletal muscle are conducted on whole tissue homogenates, essentially nothing is known about regulatory processes exclusively within muscle fibres in vivo. Utilizing a novel genetically modified mouse model developed by our laboratory, we (1) outline a simple and rapid workflow for isolating pure myonuclei from small tissue samples via fluorescent activated cell sorting and extracting high-quality large-fragment DNA for downstream analyses, and (2) provide information on myonuclear and interstitial cell nuclear CpG DNA methylation via reduced representation bisulphite sequencing (RRBS) using mice that were subjected to an acute mechanical overload of the plantaris muscle. In 3-month-old mice, myonuclei are ~50% of total nuclei in sham and ~30% in 3-d overloaded muscle, the difference being attributable to mononuclear cell infiltration and proliferation with overload. In purified myonuclei, pathway analysis of hypomethylated promoter regions following overload was distinct from interstitial nuclei and revealed marked regulation of factors that converge on the master regulator of muscle growth mTOR, and on autophagy. Specifically, acute hypomethylation of Rheb, Rictor, Hdac1, and Hdac2, in addition to a major driver of ribosome biogenesis Myc, reveals the epigenetic regulation of hypertrophic signalling within muscle fibres that may underpin the long-term growth response to loading. This study provides foundational information on global myonuclear epigenetics in vivo using RRBS, and demonstrates the importance of isolating specific nuclear populations to study the epigenetic regulation of skeletal muscle fibre adaptation.

| S-EPMC7595631 | biostudies-literature

The Myonuclear DNA Methylome in Response to an Acute Hypertrophic Stimulus

Project description:We conducted reduced representation bisulfite sequencing (RRBS) on myonuclei and interstitial nuclei and observed stark differences in methylation patterns during adaptation

2020-04-13 | GSE144774 | GEO

The rRNA epitranscriptome and myonuclear SNORD landscape in skeletal muscle fibers contributes to ribosome heterogeneity and is altered by hypertrophic stimulus

Project description:The rRNA epitranscriptome and myonuclear SNORD landscape in skeletal muscle fibers contributes to ribosome heterogeneity and is altered by hypertrophic stimulus

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Coordinated Regulation of Myonuclear DNA Methylation, mRNA, and miRNA Levels Associates with the Metabolic Response to Rapid Synergist Ablation-Induced Skeletal Muscle Hypertrophy in Female Mice

Project description:We investigatedmyonucleus-specific microRNA transcriptomes following an acute hypertrophic stimulus in mouse plantaris.

2023-11-01 | GSE245715 | GEO

The rRNA epitranscriptome and myonuclear SNORD landscape in skeletal muscle fibers contributes to ribosome heterogeneity and is altered by hypertrophic stimulus

Project description:In cell biology, ribosomal RNA (rRNA) 2'O-methyl (2'-O-Me) is the most prevalent post-transcriptional chemical modification contributing to ribosome heterogeneity. The modification involves a family of small nucleolar RNAs (snoRNAs) and is specified by box C/D snoRNAs (SNORDs). Given the importance of ribosome biogenesis for skeletal muscle growth, we asked if rRNA 2'-O-Me in nascent ribosomes synthesized in response to a growth stimulus is an unrecognized mode of ribosome heterogeneity in muscle. To determine the pattern and dynamics of 2'-O-Me rRNA, we used a sequencing-based profiling method called RiboMeth-seq. We applied this method to tissue-derived rRNA of skeletal muscle and rRNA specifically from the muscle fiber using an inducible myofiber-specific RiboTag mouse in sedentary and mechanically overloaded conditions. These analyses were complemented by myonuclear-specific small RNA sequencing to profile SNORDs and link the rRNA epitranscriptome to known regulatory elements generated within the muscle fiber. We demonstrate for the first time that mechanical overload of skeletal muscle 1) induces decreased 2'-O-Me at a subset of skeletal muscle rRNAand 2) alters the SNORD profile in isolated myonuclei. These findings point to a transient diversification of the ribosome pool via 2'-O-Me during growth and adaptation in skeletal muscle. These findings suggest changes in ribosome heterogeneity at the 2'-O-Me level during muscle hypertrophy and lay the foundation for studies investigating the functional implications of these newly identified "growth-induced" ribosomes.

2024-07-24 | GSE273053 | GEO

Transcriptome analysis following an acute loading-induced skeletal muscle growth stimulus in mice yields tools for discerning global and MYC regulatory networks

Project description:We investigated global, actively transcribed, stable, and myonucleus-specific transcriptomes following an acute hypertrophic stimulus in mouse plantaris. With these datasets we define global and Myc-specific dynamics at the onset of rapid loading-induced muscle fiber growth.

2023-05-01 | GSE213406 | GEO

Gene expression analysis in Tibialis anterior (TA) muscle upon titration of myonuclear numbers

Project description:Skeletal muscle myofibers accrue hundreds of nuclei during post-natal development via fusion with activated satellite cells (myoblasts), which is absolutely reliant on expression of the muscle fusogen myomaker (Mymk) in the myoblasts. Using an inducible genetic approach to render myoblasts non-fusogenic (by tamoxifen-inducible Pax7-CreER mediated recombination of the Mymk gene exclusively in satellite cells), we blocked myonuclear accrual at different time-points of post-natal development and thereby titrated the number of nuclei in resultant mutant myofibers. These Microarray assays were carried out on age day 28 (P28) using total RNA isolated from control and mutant muscle to determine changes in transcriptional profiles of these muscles to (a) assess effects of myonuclear titration, and (b) identify adaptive mechanisms elicited in mutant muscles in response to myonuclear deficiency. We used microarrays to generate information about transcriptional profiles in muscles with varying levels of myonuclear deficiencies.

2020-08-25 | GSE141296 | GEO

Systemic remodeling of translation efficiencies on oxygen stimulus.

Project description:Protein concentrations evolve under greater evolutionary constraint than mRNA levels. In addition, translation efficiency of mRNA populations represents the chief determinant of basal protein concentrations. This raises a fundamental question as to how mRNA and protein levels are actively coordinated in dynamic systems responding to acute physiological stimuli. This report examines the contributions of mRNA abundance and translation efficiency to protein output in cells responding to oxygen stimulus. We show that alternative translation efficiencies, not mRNA levels, represent the major adaptive mechanism that governs the cellular response to perturbations in [O2]. This phenomenon is coordinated by eIF4F under atmospheric [O2] and the previously uncharacterized hypoxic eIF4F (eIF4FH) under low [O2]. The oxygen-regulated remodeling of translation efficiency enables oxygenated and hypoxic cells to produce surprisingly divergent translatomes of similar complexity, with minimal dependence on mRNA levels. Changes in mRNA concentrations observed between normoxic and hypoxic cells are likely neutral, as they are during evolution. We propose that mRNAs contain hard-wired translation efficiency determinants for their triage by the translation apparatus on [O2] stimulus.

2016-02-05 | PXD003037 | Pride

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