Single-base detection

Credit: Courtesy of Matteo Pellegrini, University of California, Los Angeles" /> Credit: Courtesy of Matteo Pellegrini, University of California, Los Angeles Researcher: Matteo Pellegrini, assistant professor of Molecular, Cell and Developmental Biology, University of California, Los Angeles Project:

Jeffrey M. Perkel
Aug 1, 2008
<figcaption> Credit: Courtesy of Matteo Pellegrini, University of California, Los Angeles</figcaption>
Credit: Courtesy of Matteo Pellegrini, University of California, Los Angeles

Researcher:

Matteo Pellegrini, assistant professor of Molecular, Cell and Developmental Biology, University of California, Los Angeles

Project:

Mapping methylation at single-base resolution across the Arabidopsis genome.

Problem:

Existing genome-wide methylation technologies provide coarse-grained resolution. Pellegrini wanted single-base data on a genome-wide scale.

Solution:

Pellegrini and his colleagues combined bisulfite conversion - which Pellegrini calls "the gold standard" for methylation detection - with deep sequencing using Illumina's 1G Genome Analyzer.

Sodium bisulfite converts unmethylated cytosine to uracil, while leaving 5'-methylcytosine protected. PCR amplification converts the uracil to thymine, a change that is detected by sequencing both treated and untreated samples (Nature, 452:215-9, 2008). "If a read C maps to a genomic C, it was methylated, while if a read T maps to a genomic...