AI Article Synopsis
- Abnormal DNA methylation in CpG islands affects gene regulation and is linked to diseases like cancer.
- Bisulfite-based methods, such as methylation-specific PCR (MSP) and bisulfite sequencing (BiSeq), are often used to analyze this methylation but require tedious tasks for ensuring primer specificity.
- methGraph is a web application that simplifies the visualization and quality evaluation of PCR-based methylation assays, allowing researchers to assess primer specificity, map it on the genome, and generate customizable figures for publications.
Article Abstract
Abnormalities in DNA methylation of CpG islands that play a role in gene regulation affect gene expression and hence play a role in disease, including cancer. Bisulfite-based DNA methylation analysis methods such as methylation-specific PCR (MSP) and bisulfite sequencing (BiSeq) are most commonly used to study gene-specific DNA methylation. Assessing specificity and visualizing the position of PCR primers in their genomic context is a laborious and tedious task, primarily due to the sequence changes induced during the bisulfite conversion. For this purpose, we developed methGraph, a web application for easy, fast and flexible visualization and accurate in silico quality evaluation of PCR-based methylation assays. The visualization process starts by submitting PCR primer sequences for specificity assessment and mapping on the genome using the BiSearch ePCR primer-search algorithm. The next step comprises the selection of relevant UCSC genome annotation tracks for display in the final graph. A custom track showing all individual CpG dinucleotides, representing their distribution in the CpG island is also provided. Finally, methGraph creates a BED file that is automatically uploaded to the UCSC genome browser, after which the resulting image files are extracted and made available for visualization and download. The generated high-quality figures can easily be customized and exported for use in publications or presentations. methGraph is available at http://mellfire.ugent.be/methgraph/.
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| http://dx.doi.org/10.4161/epi.5.2.11161 | DOI Listing |
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