CpG context and content in evolutionary signatures of brain DNA methylation
Ontology highlight
ABSTRACT: We assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. We identified key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease. Characterization of evolutionary signatures of DNA methylation in the brain
Project description:We report a new method for genome-wide methylation profiling that is able to probe methylation status in both single-copy DNA and interspersed repeats. This method, MethylMAPS, uses methylation-sensitive and -dependent enzymes to fractionate the genome according to methylation state. Methylated and unmethylated fragments are then sequenced with Next-Gen sequencing to map methylated and unmethylated CpG sites in the genome. We have used this method to determine the methylation status of >275 million CpG sites in human and mouse DNA from breast and brain tissues. We conclude that methylation is the default state of most CpG dinucleotides and that a combination of local dinucleotide frequencies, the interaction of repeated sequences, and the presence or absence of histone variants or modifications shields a population of CpG sites (most of which are in and around promoters) from DNA methyltransferases that lack intrinsic sequence specificity. Genome-wide methylation mapping in two normal human breast tissues, human brain tissue and mouse brain tissue.
Project description:Cellular differentiation involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. We have investigated DNA genome-wide methylation dynamics in embryonic stem cells, primary myoblasts, terminal differentiated myotubes and mature myofibers. About 1.000 differentially methylated regions (DMRs) have been indentified during muscle-lineage determination and terminal differentiation. As a whole, muscle lineage commitment was characterized by a major gain of DNA methylation, while muscle differentiation was accompanied by loss of DNA methylation in CpG-poor regions. Notably, hypomethylated regions in muscle cells were neighboured by enhancer-type chromatin, suggesting the involvement of DNA methylation in the regulation of cell-type specific enhancers. Indeed, one of the hypomethylations detected in muscle cells affected the super-enhancer of the master transcription factor Myf5. Super-enhancers have been defined as large clusters of transcriptional enhancers driving cell-identity and gene expression, but how these lineage-specific super-enhancers are specifically activated or repressed in different tissues is not well understood. We demonstrated that the binding of the transcription factor USF1 to Myf5 locus occurs upon DNA demethylation of the super-enhancer region in myogenic committed cells. Taken all together, we have characterized the unique DNA methylation signatures of muscle-committed cells and highlighted the importance of DNA methylation mediated regulation of cell identity super-enhancers. We have investigated DNA genome-wide methylation dynamics in embryonic stem cells, primary myoblasts, terminal differentiated myotubes and mature myofibers by AIMS-seq techniques and coupled to microarray expression data by SurePrint G3 Mouse 8x60K from Agilent Technologies. Samples were in triplicates, except for ESCs (quadruplicates).
Project description:Lung adenocarcinoma’s genomic alterations exhibit vast variation. Lung adenocarcinoma also has previously described intrinsic gene expression subtypes (Hayes et al. 2006, PMID: 17075127). This study detect global methylation differences among gene expression subtypes. These specimens were also assayed for genomewide transcription in GSE26939 and copy number in GSE36363. 33 tumor samples and 10 normal samples were quantified for DNA methylation by MSNP (Yuan et al, PMID: 16585166) using Affymetrix SNP 250K_StyI microarrays.
Project description:We assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. We identified key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease.
Project description:To improve our understanding of the relationships between methylation and expression we profiled mRNA expression and single-base resolution methylation levels for two breast cancer cell lines, MCF7 and T47D. Expression was profiled using RNA-seq. Methylation was assayed using Methyl-MAPS, which uses methylation-sensitive and -dependent restriction enzyme digests followed by high-throughput sequencing to identify methylation levels at individual CpGs (Edwards et al. 2010, Genome Research). DNA Methylation was assayed for two breast cancer cell lines using Methyl-MAPS.
Project description:The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 currently has three remaining un-sequenced gaps on its q-arm. All three gaps are within gene-dense regions, or overlap loci associated with human disorders, including one gap, which is at DLGAP4. In this study we sequenced, determined the complete sizes and assessed epigenetic landscapes of all three un-sequenced gaps on human chromosome 20 using a methodological approach involving Sanger sequencing, mate-pair paired-end high-throughput sequencing and chromatin and methylation analysis. We found histone H3K27me3 to be distributed across all three gaps in immortalized B-lymphocytes. We found five novel CpG islands in one gap to be highly hypermethylated in genomic DNA from both peripheral blood lymphocytes and human cerebellum. One of these CpG islands was differentially methylated and paternally hypermethylated. Furthermore, computational analyses predicted the presence of structured non-coding RNAs (ncRNAs) in all three chromosome 20 gaps. We verified expression for thirteen candidate ncRNAs, some of which showed tissue-specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated expression particularly in the human brain. Our data suggests that un-sequenced human genome gaps may comprise functional elements. Mate-pair paired end sequencing using genomic DNA from human translocation carriers having chromosomal rearrangments of chromosomes other than chromosome 20 and chromatin, DNA methylation analysis using human peripheral blood lymphocytes and/or human cerebellum tissue. Analysis done for three remaining human chromosome 20 un-sequenced gap regions.
Project description:DNA methylation profiling of cancer and control samples. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across 1,505 CpG sites CpGs distributed across 807 genes in blood DNA specimens. DNA samples were extracted from blood specimens, bisulfite treated and subsequently used for GoldenGate Methylation Cancer Panel I Array (Illumina) according to manufacturer’s protocol together with normalization methylated, hemimethylated and unmethylated DNA controls (Qiagen).
Project description:Cancer cells have an altered distribution of DNA methylation and express aberrant DNA methyltransferase 3B transcripts, which encode truncated proteins. To test if a truncated DNMT3B isoform disrupts DNA methylation in vivo, we constructed transgenic mice expressing DNMT3B7, a common truncated DNMT3B isoform in cancer cells. DNMT3B7 transgenic mice exhibit altered embryonic development, including lymphopenia, craniofacial abnormalities, and cardiac defects, similar to Dnmt3b-deficient animals, but rarely develop cancer. However, DNMT3B7 expression increases the frequency of mediastinal lymphomas in Eμ−myc animals. Eμ-myc/DNMT3B7 lymphomas have more chromosomal rearrangements, increased global methylation levels, and more locus-specific perturbations in DNA methylation patterns compared to Eμ-myc lymphomas. Our results demonstrate that a truncated DNMT3B protein can alter tumorigenesis, suggesting a similar role in human tumors. Direct comparison of DNA methylation in lymphoma samples from Eu-Myc vs Eu-Myc/Dnmt3b7 mice.
Project description:DNA methylation and DNA replication timing were examined across a variety of human tissues and cell lines, applying microarray-based techniques. The analyses revealed that late-replicating DNA was demethylated compared to the methylation of early-replicating regions. DNA methylation: Epstein-Barr-Virus (EBV) transformed B-lymphocyte cell lines GM10849, GM12089, GM12092, GM12093, and GM08714 (ICF) (http://ccr.coriell.org/nigms) were cultured in RPMI-1640 supplemented with 15% FCS (Sigma) at 37oC and 5% CO2. Normal BJ foreskin fibroblasts (NHF cells) at different PDs (36)(34) were cultured in 4:1 DMEM : M-199 supplemented with 15% FCS (Sigma) at 37oC and 5% CO2. Replication timing: EBV-transformed female B-lymphocyte cell lines GM12092 and GM12093 were cultured as above, harvested from logarithmic growth cultures, washed once in ice-cold phosphate-buffered saline, immediately fixed in 70-85-95% ethanol at -20oC, stained with propidium iodide, and sorted into G1 and early-S fractions using a MoFlo cell sorter.