Hey, sometimes more really is, well, more. Lately in the sequencing arena, we’ve heard a lot about some really slick advances in targeted sample enrichment and other ways to sequence less real estate in exchange for more coverage and better data. Such enrichment methods should be equally useful to epigenetics as they are in current re-sequencing applications.
But, as we have learned from non-coding RNAs, caution should be taken when assuming which genomic regions are important and which aren’t. Maybe the stuff you’re not sequencing IS interesting after all. Just last week, a talented crew of researchers from Harvard and the Broad Institute showed the importance of looking at DNA methylation in genomic regions outside the usual suspects ( e.g. promoters, TSSs etc.,) and showed us a couple of different approaches for analyzing DNA methylation in these regions.
- The first method makes use of bisulfite padlock probes (BSPPs) to interrogate specific CpGs across the genome. Since the BSPPs are extremely specific, thousands of them can be used at once to create libraries suitable for massively parallel sequencing.
- The second method, called methyl sensitive cut counting (MSCC) allows for genome-wide methyaltion profiling. Using the methylation sensitive restriction enzyme HpaII to cut throughout the genome creates an unbiased library that can then be sequenced. Each of the 1.4 million HpaII cut locations can then be analyzed for methylation status.
The team profiled several human cell lines using both methods, which proved to be complementary, and generated data that correlated well to each other as well as to other existing data from expression and ChIP studies. They found what may be a general pattern of highly expressed genes having low promoter methylation and high gene-body methylation. They also observed differential methylation in promoters with intermediate CpG density, as well as in regions outside of CpG islands or promoters.
All of these findings serve to highlight how useful these more open interrogation methods are for profiling DNA methylation in genomic areas that are otherwise missed. For the full scoop on these methods go to. Nature Biotechnology, March 2009.