Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Methylation profiling of human type 2 diabetes patients to screen for genes differentially methylated in T2DM MeDIP ARRAY_NGT_vs_T2DM

ABSTRACT: Here, we performed a genome-wide promoter analysis of DNA methylation to screen for genes differentially methylated in T2DM.
We used methylated DNA immunoprecipitation (MeDIP), combined with microarray technology (Keshet et al., 2006; Weber et al., 2005), to discover whether changes in DNA methylation are specific to T2DM. A cohort of normal glucose tolerant (NGT) and Type 2 diabetic (T2DM) male volunteers was studied.

ORGANISM(S): Homo sapiens

DISEASE(S): NGT

SUBMITTER: Romain Barres

PROVIDER: E-MEXP-2253 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Non-CpG methylation of the PGC-1alpha promoter through DNMT3B controls mitochondrial density.

Barrès Romain R Osler Megan E ME Yan Jie J Rune Anna A Fritz Tomas T Caidahl Kenneth K Krook Anna A Zierath Juleen R JR

Cell metabolism 20090901 3

Epigenetic modification through DNA methylation is implicated in metabolic disease. Using whole-genome promoter methylation analysis of skeletal muscle from normal glucose-tolerant and type 2 diabetic subjects, we identified cytosine hypermethylation of peroxisome proliferator-activated receptor gamma (PPARgamma) coactivator-1 alpha (PGC-1alpha) in diabetic subjects. Methylation levels were negatively correlated with PGC-1alpha mRNA and mitochondrial DNA (mtDNA). Bisulfite sequencing revealed th ...[more]

PMID: 19723495

Similar Datasets

Genome wide DNA methylation changes with age in disease free human skeletal muscle

Project description:A decline in skeletal muscle mass and function with aging is well recognized, but remains poorly characterized at the molecular level. Here we report for the first time a genome-wide study of DNA methylation dynamics in skeletal muscle of healthy male individuals during normal human aging. We predominantly observed hypermethylation throughout the genome within the aged group as compared to the young subjects. Differentially methylated CpG (dmCpG) nucleotides tend to arise intragenically, and are underrepresented in promoters and are overrepresented in the middle and 3’ end of genes. The intragenic methylation changes are over represented in genes which guide the formation of the junction of the motor neuron and myofibers. We report a low level of correlation between previous gene expression studies of aged muscle with our current analysis of DNA methylation status. For those genes that had both changes in methylation and gene expression with age, we observed a reverse correlation, with the exception of intragenic hypermethylated genes, that were correlated with increased gene expression. We argue that a minimal number of dmCpG sites or select sites are required to be altered in order to correlate with gene expression changes. Finally, we identified 500 dmCpG biomarkers that perform well in a prediction of human biological age within our cohorts. Our findings highlight epigenetic links between aging post-mitotic skeletal muscle and DNA methylation. 48 experimental samples (24 young and 24 older individuals) were used overall. There were 4 replicates per group.

2013-12-03 | E-GEOD-50498 | biostudies-arrayexpress

The zebrafish runzel mutant results in a novel muscular dystrophy phenotype due to a titin mutation

Project description:The zebrafish runzel (ruz) carries a mutation in the titin gene resulting in muscle degeneration and embryonic lethality. At the onset of the visible phenotype (3-3.5 days post fertilization), RNA expression of the tail and trunk (primarily skeletal muscle) was compared between ruz mutants and wildtype siblings using the Affymetrix Zebrafish Gene Chip. Mutant RNA was matched with RNA of wildtype siblings from the same clutch. 3 separate clutches were used (n=3). RNA was labeled, sheered, and hybridized as in Shephard et al. (Shepard et al., 2005) and the data analyzed as in Choe et al. and Weber et al. (Choe et al., 2005; Weber et al., 2005). Results suggest a novel mechanism of titin muscular dystrophy pathogenesis including upregulation of heat shock proteins. Keywords: disease state analysis

2006-07-30 | GSE4585 | GEO

A mitochondrial proteome profile of type 2 diabetes mellitus in skeletal muscles

Project description:The goal of the project is to understand the mitochondrial proteome profiles related to T2DM. We performed comprehensive proteome profiling of mitochondria isolated from skeletal muscles in nine T2DM patients and nine control subjects with normal glucose tolerance (NGT).

2018-10-02 | PXD004312 | Pride

Methylome analysis of congenital ectopic thyroids

Project description:To assess whether specific genes have relevant somatic genetic or epigenetic alterations in ectopic tissue, we used a combined analysis of transcriptome (confirmed by qRT-PCR on 68 genes), methylome, structural genome variations (copy number variants, CNVs) and miRNA profile of ectopic compared with orthotopic thyroids. The MeDIP-chip was performed using pair of enriched methylated fraction (IP) and nomal fraction (IN) of genomic DNA from the three available cases and the three controls. The methylated fraction of genomic DNA was enriched using the methylated DNA immunoprecipitation (MeDIP) assay (Weber et al. Nat Genetics, 2005) and interrogated on human Promoter plus CpG Island Tiling Arrays with a ChIP design for CpG islands and promoter regions (n=28,226) from HG18 using 385,020 Probes selected from CGH probe bank with a median spacing of 101bp (Roche NimbleGen, Madison, WI).

2010-10-27 | E-GEOD-17581 | biostudies-arrayexpress

Global analysis of lysine acetylation reveals its role in multiple biological processes in Glycine max

Project description:Glycine max was cultivated in China for nearly 5000 years, commonly referred to as soybeans, now it has become one of the important economic crops in the world (Li et al., 2008). Post-translational modifications are known to regulate many cellular processes, which are dynamic and reversible and can make protein functions changed.(Westermann and Weber, 2003). To date, among 400 PTMs have been detected, such as Acetylation, Ubiquitination, Phosphorylation, Malonylation, Succinylation and Methylation(Colak et al., 2013; Weinert et al., 2013).

2020-11-16 | PXD021246 | Pride

Exercise Training Effects on Human Skeletal Muscle DNA Methylation

Project description:This study aimed to determine skeletal muscle DNA methylation changes in a cohort of volunteers with a range of insulin sensitivities following 8-weeks of supervised exercise training. We studied 13 sedentary participants (5M/8F, 34.6 ± 3.1 years) and performed euglycemic hyperinsulinemic clamps with 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.

2022-03-01 | E-MTAB-11282 | biostudies-arrayexpress

DNA methylation analysis of human skeletal muscle after endurance training

Project description:Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. Training effects were mirrored by significant alterations in DNA methylation and gene expression in regions with a homogeneous muscle energetics and remodeling ontology. Differential DNA methylation predominantly occurred in regulatory enhancer regions, where known binding motifs of MRF, MEF2 and ETS proteins were identified. A transcriptional network analysis revealed modules harboring distinct ontologies, and interestingly the overall direction of the changes of methylation within each module was inversely correlated to expression changes. In conclusion, we show that highly consistent and associated modifications in methylation and expression, concordant with observed health-enhancing phenotypic adaptations, are induced by a physiological stimulus. DNA samples from vastus lateralis muscle bisopsies were included in the study. Specifically, 23 subjects performed three months of supervised endurance training. Biospies were taken at rest, before and after training. DNA methylation levels were profiled using Illumina 450K arrays.

2014-11-04 | E-GEOD-60655 | biostudies-arrayexpress

A mitochondrial proteome profile of type 2 diabetes mellitus in skeletal muscles

2019-03-13 | MSV000083560 | MassIVE