Profiling Exon Methylation with Liquid Hybridization Capture-Based Bisulfite Sequencing

Sometimes, you just want to get to the good stuff right away. Now, researchers in China report that they’ve developed a way to target their sequencing when analyzing methylomes rather juggling 6 hard drives. With their new liquid hybridization capture-based bisulfite sequencing (LHC-BS) method, they just grab exons and analyze them for methylation. The method is quicker and less expensive than whole-genome methods and much more practical for a clinical lab to use.

The researchers enriched for exons with biotinylated RNA probes in a liquid hybridization platform, which meant they only had to use 2-3 µg of genomic DNA (instead of the 20 µg required for an array-based capture method).

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They fragmented the genomic DNA and created adapter-ligated libraries that hybridized with the RNA probes. After retrieving the target exon fragments with streptavidin-coated beads, the researchers treated the exons with sodium bisulfite, did a PCR amplification, and sequenced them.

LHC-BS gave them good exon coverage (more than 97%) for DNA in a human blood sample and in a cell line without doing a ton of sequencing. And the methylation results were just as good as the results they’d gotten with whole-genome bisulfite sequencing.

The method isn’t necessarily just for exons, either. “The technique is highly sensitive and flexible and can be applied to identify differentially methylated regions (DMRs) at specific genomic locations of interest, such as regulatory elements or promoters,” say the researchers.

For the full scoop, read BMC Genomics, December 2011.