MethPrimer: designing primers for methylation PCRs

TLDR

DNA methylation is an epigenetic regulatory mechanism, and bisulfite‑conversion PCR methods such as BSP and MSP are widely used, but existing primer‑design tools cannot accommodate the sequence changes and constraints introduced by bisulfite treatment. The authors developed MethPrimer to address this gap. MethPrimer takes a DNA sequence, identifies CpG islands, and selects primers around these islands or user‑specified regions. MethPrimer, built on Primer3, successfully designs primers for BSP and MSP and presents results in text and graphic form via a web interface. MethPrimer is freely available at http://itsa.ucsf.edu/~urolab/methprimer and can be contacted at [e-mail].

Abstract

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 DNA sequence context caused by bisulfite treatment and many special constraints both on the primers and the region to be amplified for such experiments. Therefore, the present study was designed to develop a program for such applications. Results: MethPrimer, based on Primer3, is a program for designing PCR primers for methylation mapping. It first takes a DNA sequence as its input and searches the sequence for potential CpG islands. Primers are then picked around the predicted CpG islands or around regions specified by users. MethPrimer can design primers for BSP and MSP. Results of primer selection are delivered through a web browser in text and in graphic view. Availability: MethPrimer is freely accessible at the following Web address http://itsa.ucsf.edu/~urolab/methprimer Contact: [e-mail]@aol.com To whom correspondence should be addressed.