Genome-wide changes in DNA methylation in response to physical exercise
ABSTRACT: Here we describe a genome-wide analysis of DNA-methylation in muscle of trained mice. In comparison to sedentary controls 2762 genes exhibited differentially methylated CpGs in their putative promoter regions. The majority of these genes were related to muscle growth and differentiation and a minor fraction involved in metabolic regulation. These findings suggest that DNA-methylation is involved in the regulation of muscle adaptation to regular exercise training. Reduced representation bisulfite sequencing of murine quadriceps muscle
Project description:Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T-lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in brain cells. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites, implicating a mechanism involving altered transcription factor binding. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning. Examination of methylation changes in two mouse models of Down syndrome with sub-chromosomal duplications, Dp(10)1Yey and Dp(16)1Yey, compared to one littermate wild type mouse using whole genome bisulfite sequencing.
Project description:Differential hyper- and hypo-methylation regions in G0 versus G4/G5 CMP The goal of this study is to evaluate changes in CpG methylation profilings of telomere dysfunctional common myeloid progenitor cells (CMP) as compared to their wild type controls Genomic DNA was extracted from sorted CMP populations isolated from 3 pools of G0 or 2 pools of G5 mice using UltraPure Phenol:Chloroform:Isoamyl Alcohol according to manufacturer’s instructions (Life Technologies). 14,000 to 30,000 cells were available for each sample, resulting in a minimum of 45ng of DNA. Genome-wide DNA methylation profiling was performed by RRBS. Library preparation and sequencing were performed at the UT MD Anderson Cancer Center’s DNA Methylation Analysis Core and Sequencing and Microarray Facility, according to published protocols. RRBS sequencing data were aligned and methylation was called using Bismark v0.7.119. In brief, bisulphite-treated DNA was aligned to UCSC Genome Browser mm10 reference genome using Bowtie. In total 29-38 million reads were generated per sample with alignment rates around 63%. Next, MethylKit10 implemented with Fisher’s exact test was used to compare the cytosine methylation profiles of G0 and G5 CMP. Gene promoter regions were calculated based on RefSeq gene annotations with regions starting 1 kb upstream of the annotated transcription start site (TSS) and extending 500 base pairs downstream of TSS. Exons, introns, and CpG islands coordinates were collected from the UCSC Genome Browser mm10 version.
Project description:The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins. Methyl-seq analysis for undifferentiated induced pluripotent stem cell (iPSC) lines (n = 21), human dermal fibroblast (HDF, n = 1), human peripheral blood (n = 1), and human keratinocyte (n = 1), and ATAC-seq analysis for 2 iPSC lines and an embryonic stem cell (ESC) line with two different culture conditions. CTCF-ChIP-seq analysis for an ESC line.
Project description:These data are a component of a larger study investigating differences in gene regulation in relationship to rhesus macaque dominance rank. These data compare DNA methylation levels between individuals of different rank on a genome-wide scale using bisulfite sequencing DNA from peripheral blood mononuclear cells sampled from 3 high ranking individuals and 3 low ranking individuals (all adult female rhesus macaques)
Project description:Seasonal photoperiodic changes have strong impact on development in Nasonia vitripennis. Here, Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps of female wasps maintained in long vs short day. We have identified differential methylated loci that encode the photoperiodic change. analysis of DNA methylation in female wasps maintained in long vs short day, using RRBS followed by Illumina sequencing
Project description:We report the generation and analysis of high-throughput DNA methylation profiles at nucleotide resolution in a subset of targeted gene trap mouse mutants. Using high-throughput sequencing of bisulfite treated DNA, we generated DNA methylation percentage for CpG islands, and LacZ (reporter) gene in mice with the apparent silencing of the targeted gene promoter reflected by reduced reporter mRNA level. These results were contrasted with findings for a set of mutants with no silencing or CpG methylation following targeted mutagenesis using the same gene trap vector. Our findings supports the hypothesis that presence of the exogenous DNA in the targeting vector may influence the expression of genes in close proximity or may lead to promoter silencing of the target where the promoter is marked by CpG methylation. Examination of CpG methylation profiles in Knock-out and wild type mice We evaluated targeted gene promoter silencing in a group of six mutants carrying the tm1a Knockout Mouse Project allele containing both a LacZ reporter gene driven by the native promoter and a neo selection cassette. Methylation of the promoter CpG islands and LacZ coding sequence were evaluated by sequencing of bisulfite-treated DNA. CpG Islands (samples labeled as CpG) and trans gene (samples labeled as LacZ) were amplified after Bisulfite treatment. Please note that the same gDNA was used to amplify CpG Island (Gene_CpG_KO ) and LacZ (Gene_LacZ_KO) reporter for the same gene. PCR product of amplification was gel separated, isolated and pooled. After libraries were prepared and sequenced, the alignment was performed. CpG island and LacZ alignments were done separately resulting in three different Processed Data files per gene investigated: Gene_CpG_KO, Gene_LacZ_KO and Gene_CpG_WT. LacZ reference is included in the submission, but is also available for download from KOMP Phenotype website (www.kompphenotype.org). Also please note that the libraries were prepared using Illumina TruSeq RNA Sample Prep Kit starting from adapter binding step as samples were double stranded Bisulfite treated DNA amplicons. So the library preparation was done as with RNASeq, but samples investigated were bisulfite treated.
Project description:Our data show Satb1 deficiency leads to alterations in DNA cytosine methylation and a commitment-primed epigenetic state in HSCs. Examination of DNA cytosine methylation in wild type HSC and differentiation-committed progenitors as well as in wild type HSC and HSC lacking Satb1 (n=2 each).
Project description:Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are driver mutations in acute myeloid leukemia (AML) and other cancers. We report the development of new allosteric inhibitors of mutant IDH1. Crystallographic and biochemical results demonstrated that compounds of this chemical series bind to an allosteric site and lock the enzyme in a catalytically inactive conformation, thereby enabling inhibition of different clinically relevant IDH1 mutants. Treatment of IDH1 mutant primary AML cells uniformly led to a decrease in intracellular 2-HG, abrogation of the myeloid differentiation block and induction of granulocytic differentiation at the level of leukemic blasts and more immature stem-like cells, in vitro and in vivo. Molecularly, treatment with the inhibitors led to a reversal of the DNA cytosine hypermethylation patterns caused by mutant IDH1 in AML patients’ cells. Our study provides proof-of-concept for the molecular and biological activity of novel allosteric inhibitors for targeting different mutant forms of IDH1 in leukemia. To obtain insight into the molecular mechanism of the novel IDH1 mutant allosteric inhibitor, primary AML cells were treated with either GSK321 IDH1 active inhibitor or Controls (DMSO or GSK990 inactive inhibitor) followed by DNA extraction for ERRBS analysis. Primary IDH1 mutant acute myeloid leukemia (AML) mononuclear (MNC) cells were treated in suspension cultures in differentiating media for 6 days with 3 microM GSK990 or GSK321 and an equal volume of DMSO, Followed ERRBS analysis after DNA extraction.
Project description:Obesity is a heritable disorder, with children of obese fathers at higher risk of developing obesity. Environmental factors epigenetically influence somatic tissues, but the contribution of these factors to the establishment of epigenetic patterns in human gametes is unknown. Here, we hypothesized that weight loss remodels the epigenetic signature of spermatozoa in human obesity. Comprehensive profiling of the epigenome of sperm from lean and obese men showed similar histone positioning, but small non-coding RNA expression and DNA methylation patterns were markedly different. In a separate cohort of morbidly obese men, surgery-induced weight loss was associated with a dramatic remodeling of sperm DNA methylation, notably at genetic locations implicated in the central control of appetite. Our data provide evidence that the epigenome of human spermatozoa dynamically changes under environmental pressure, and offers insight into how obesity may propagate metabolic dysfunction to the next generation. Examination of the DNA methylation status, histone retention and sncRNA expression of the semen of 13 lean and 10 obese individuals; as well as the DNA methylation status of the semen of 6 obese men undergoing Roux-en-Y GBP surgery, at three time points: approximately 1 week before, 1 week after and 1 year after the surgery.
Project description:Placental gene expression is a finely controlled process, yet little is known about the factors that regulate it, including epigenetic factors such as DNA methylation. In this study, we quantified the effects of DNA methylation on placental gene expression. Using targeted high throughput sequencing, we generated methylation profiles of 3.7 million CpG dinucleotides from 6 karyotypically normal CVS samples and compared these to gene expression data obtained from a publically available database. We found a broad association between methylation and gene expression at both the chromosome and individual gene levels. At the chromosome level, we found alternating domains of high and low methylation. Within each gene, we found distinct methylation patterns at different regulatory genetic elements. For example, the promoters of highly expressed genes were neither highly methylated, nor completely unmethylated. Rather, they had < 50% of the CG dinucleotides in their sequences in the methylated state. In contrast, promoters of unexpressed genes tended to be either highly methylated or fully unmethylated. Similarly, patterns of methylation in exons and introns differed between highly expressed and unexpressed genes. Our data show that the relationship between DNA methylation and gene expression is nuanced: highly expressed and unexpressed genes differ, not only by their extent of methylation, but also by minute changes in the locations of their methylation sites. DNA methylation analysis of placental genes may help predict abnormal placental gene expression and pregnancy complications, making it a possible tool for prenatal diagnosis. DNA from 6 chorionic villus samples from the 1st trimester (from 3 male and 3 female fetuses) as well as 3 maternal blood cell samples was extracted, hybridized to probes in the Agilent SureSelectXT Methyl-Seq Target Enrichment kit, targeting 84Mb of the genome and then bisulfite converted before sequencing.