PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands

Predicting CpG Islands and DNA Methlation in the Cow Genome Using DNA Microarray Meta-Analysis and Genome Wide Scanning

DNA methylation is a type of epigenetic changes that directly affects DNA. In mammals, DNA methylation is essential for fetal development and stem cell differentiation and this phenomenon essentially occurs within the CpG islands. In this study, two methods were used to study the DNA methylation profile of cow genome. In the first method, the DNA methylation profile of the differentially expres...

High-throughput Primer and Probe Design for Genome-Wide DNA Methylation Study Using PRIMEGENS

MethPrimer: designing primers for methylation PCRs

MOTIVATION DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP), remain the most commonly used techniques for methylation mapping. Existing primer design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based PCRs due to changes in ...

Susceptibility of nonpromoter CpG islands to de novo methylation in normal and neoplastic cells.

BACKGROUND Many cancers display alterations in methylation patterns of CpG islands--stretches of DNA rich in CpG dinucleotides often associated with gene promoters that are involved in initiation of gene transcription. This methylation may perturb expression of genes critical to the regulation of cell proliferation. Aberrant methylation is not limited to a few genes or to promoter regions but h...

CpG Islands Undermethylation in Human Genomic Regions under Selective Pressure

DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG island...