Project description:We provide the genome-wide methylome surveys of three species of deep-sea polychaete worms using Oxford Nanopore data: the siboglinids Paraescarpia echinospica and Ridgeia piscesae, and the alvinellid Paralvinella palmiformis. We characterised 5mCpG methylation in order to test hypotheses about the putative role of DNA methylation in these species.
Project description:Methylation of Hepatitis B Virus (HBV) DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection of 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we developed a method for the detection of 5mCpG on the HBV genome that does not rely on bisulfite conversion or PCR. Moreover, using the developed technique, we have provided the first de novo assembly of native HBV DNA, as well as the first landscape of 5mCpG from native HBV sequences
Project description:Identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. Cytosine methylation in CpG context (5mCpG) and cytosine hydroxymethylation (5hmCpG) are DNA modifications that identify stable cell phenotypes. To assess transition states in Th cells, we developed a method based on Cas9-targeted single molecule nanopore sequencing and found that 5mCpG can be used as markers of cellular identity. Targeting as few as 10 mouse selected genomic loci, we were able to distinguish major differentiated T cell subtypes as well as intermediate phenotypes by their native DNA 5mCpG patterns. Moreover, by using off-target sequences we were able to infer transcription factor activities relevant to each cell subtype. Our data highlight the potential to exploit native DNA methylation profiling to study physiological and pathological Th transition states.
Project description:Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human hepatocyte-like progenitor cell line HepaRG, before and after in vitro differentiation, using long-read nanopore sequencing.
Project description:Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context. The main aim of this work was to develop and validate a novel tool for determining methylation of mtDNA and to corroborate its existence across different biological contexts. Here, we profiled the human cell lineHEK 293T, before and after oxidative stress, using long-read nanopore sequencing.
Project description:Genome wide DNA methylation profiling of MZ twins discordant and concordant for BMI. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs. Samples included 30 MZ twin pairs discordant for BMI and 10 pairs concordant for BMI.
Project description:The goal of the study was to investigate if DNA methylation is associated with Lewy body pathology in human brain tissue. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in postmortem human frontal cortex samples from European donors in the Netherlands Brain Bank. Following quality checks, sample filtering and normalization, association between CpG methylation and Braak alpha-synuclein stage was assessed using linear models.
