Homo sapiens
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PROVIDER: PRJNA326399 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation on type-specific human skeletal muscle fibers
| PRJNA326906 | ENA
Project description:Purpose: Reduced Representation Bisulfite Sequencing (RRBS) DNA input requirements become a challenge when working with small pools of tissue-specific cell types. We describe an application of the RRBS method to assess DNA methylation on low-DNA input from human slow-twitch (MHC I) and fast-twitch (MHC IIa) skeletal muscle fibers. Methods : Fiber-type specific (MHC I and MHC IIa muscle fibers) total DNA was extracted from vastus lateralis muscle biopsies of 8 young physically active men (~25 yrs). A total of 16 DNA samples were generated : 8 DNA samples from pure MHC I and 8 DNA samples from pure MHC IIa muscle fibers. An equal quantity of DNA (4 ng) from each sample was combined to generate a "pooled" DNA sample representing all 8 subjects for each fiber type. Two fiber-type specific "pooled" samples of 32 ng of DNA were generated for library construction and sequencing, creating a Type 1 (MHC I muscle fibers) and Type 2a (MHC IIa muscle fibers) sample. Sequencing was performed using the HiSeq 2500 (Illumina) with 50 bp paired-end read parameters. Minimum sequencing read coverage of 5 (5x) was used as the cutoff for CpG-sites inclusion in the DNA methylation analysis. Fisher’s exact test was performed on CpG-sites that overlapped (i.e. identified in both samples) Type 1 and Type 2a samples to obtain p-values that indicate the likelihood of the site being a differentially methylated CpG-site (DMS). DMS with p<0.05 were classified as hypermethylated or hypomethylated if they were more or less methylated than the Type 1 sample, which was used as the reference sample. Results: The 32 ng of DNA from fiber-type specific muscle samples (Type 1 and 2a) used in this study ensured similar sequencing quality as compared to other studies using greater DNA input (>50 ng). Mapping ratios of ~47% and bisulfite conversion rates of ~97-98% were obtained.The unique and best alignment was successfully assessed for each of 17,376,728 CpG-sites in the Type 1 sample and 17,006,993 in the Type 2a sample, which represents ~30% of the total CpG number in the human genome. We identified 143,160 differentially methylated CpG-sites (DMS) across 14,046 genes among MHC I and MHC IIa muscle fibers. The analysis revealed that some genes predominantly expressed in MHC I were hypermethylated in MHC IIa muscle fibers. Conclusion: This study validates a low-DNA input RRBS method for human skeletal muscle samples to investigate the methylation patterns at a fiber-type specific level. These are the first fiber-type specific methylation data reported from human skeletal muscle. Considering the metabolic and structural differences between MHC I and MHC IIa muscle fibers, this technique could provide novel insights into the skeletal muscle methylation profile in relation to health, performance, disease or disuse.
2017-01-10 | GSE83741 | GEO
Project description:DNA methylation analysis of human skeletal muscle after endurance training
| PRJNA259207 | ENA
Project description:Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs.
2011-08-25 | GSE23936 | GEO
Project description:RNA-seq was performed to investigate the role of Rrm2b in skeletal muscle. Type II skeletal muscle fibers were collected from wild-type (C57BL/6) mice and two Rrm2b knockout models, the skeletal muscle-specific knockout (Rrm2b F/F;HSA-Cre, smKO) and satellite cell-specific knockout (Rrm2b F/F;Pax7-CreERT2, scKO).
2022-07-25 | E-MTAB-11318 | biostudies-arrayexpress
Project description:Skeletal muscle is an inherently heterogenous tissue comprised primarily of myofibers, which are historically classified into three distinct fiber types in humans: one “slow” (type 1) and two “fast” (type 2A and type 2X), delineated by the expression of myosin heavy chain isoforms (MYHs). However, whether discrete fiber types exist or whether fiber heterogeneity reflects a continuum remains unclear. Furthermore, whether MYHs are the main classifiers of skeletal muscle fibers has not been examined in an unbiased manner. Through the development and application of novel transcriptomic and proteomic workflows, applied to 1050 and 1038 single muscle fibers from human vastus lateralis, respectively, we show that MYHs are not the principal drivers of skeletal muscle fiber heterogeneity. Instead, ribosomal heterogeneity drives the majority of variance between skeletal muscle fibers in a continual fashion, independent of slow/fast fiber type. Furthermore, whilst slow and fast fiber clusters can be identified, described by their contractile and metabolic profiles, our data challenge the concept that type 2X are phenotypically distinct from other fast fibers at an omics level. Moreover, MYH-based classifications do not adequately describe the phenotype of skeletal muscle fibers in one of the most common genetic muscle diseases, nemaline myopathy. Our data question the currently accepted model of multiple distinct fiber types based on the expression of MYHs in humans and identifies ribosomal heterogeneity as a major driver of skeletal muscle fiber heterogeneity, opening a new field of research within skeletal muscle physiology.
2025-02-27 | PXD046863 | Pride
Project description:Skeletal muscle is an important organ for health and movement, largely driven by specific muscle fibres. However, the assessment of fibre-type-specific DNA methylation in human skeletal muscle has been limited. We generated methylome profiles of Type I muscle fibres (T1), Type II muscle fibres (T2) and whole skeletal muscle (WM) from males and females before and after 12 weeks high intensity interval training. We compared the TI and TII pooled fibre samples (per individual) and whole muscle samples at the baseline timepoint and generated TI, TII and WM profiles of human skeletal muscle from both males and females.
2025-10-23 | GSE304045 | GEO
Project description:Skeletal muscle plays an important role in the health-promoting effects of exercise training, yet the underlying mechanisms are not fully elucidated. Proteomics of skeletal muscle is challenging due to presence of non-muscle tissues and existence of different fiber types confounding the results. This can be circumvented by analysis of pure fibers; however this requires isolation of fibers from fresh tissues. We developed a workflow enabling proteomics analysis of isolated muscle fibers from freeze-dried muscle biopsies and identified >4000 proteins. We investigated effects of exercise training on the pool of slow and fast muscle fibers. Exercise altered expression of >500 proteins irrespective of fiber type covering several metabolic processes, mainly related to mitochondria. Furthermore, exercise training altered proteins involved in regulation of post-translational modifications, transcription, Ca++ signaling, fat, and glucose metabolism in a fiber type-specific manner. Our data serves as a valuable resource for elucidating molecular mechanisms underlying muscle performance and health. Finally, our workflow offers methodological advancement allowing proteomic analyses of already stored freeze-dried human muscle biopsies.
2020-12-21 | PXD012824 | Pride
Project description:Genome wide DNA methylation changes with age in disease free human skeletal muscle
| PRJNA217793 | ENA