RRBS Dives Deep into Zebrafish Brain Methylomes

Get ready for the Zebrafishnado!  OK, a tornado filled with cute little aquarium fish isn’t nearly as terrifying as a Sharknado, but a whirlwind of new data on zebrafish methylomes did reveal that their DNA methylation patterns are pretty unique compared to other species, including humans.

Scientists from New Zealand realized that no one had put together an in-depth methylome at base-pair resolution for zebrafish yet, even though most of the other model popular organisms (and even humans) had gotten the treatment.

Previous studiees had done whole-genome bisulfite sequencing (which is pricey) or MeDIP (which doesn’t get down to single base-pair res) on zebrafish. So the Kiwi team turned to a high-res, cost-effective method—reduced representation bisulfite sequencing (RRBS)—to profile the zebrafish brain methylome. Here’s some of what they found:

• CpGs occur more often in the zebrafish genome than in humans and mice, but the researchers got much less enrichment of those sites with RRBS for zebrafish versus mammals. This could be because zebrafish don’t have as many MspI sites.
• The zebrafish brain (and liver) fragments were mostly hypermethylated; for humans, this was the opposite—most of those libraries are hypomethylated.
• Unlike human RRBS libraries that have lots of CpG islands, zebrafish had more CpG island shores.

As it turns out, we’re not all that similar to zebrafish, which may not be too surprising, but the team says that there’s still a lot they can learn from the study.

“Our analysis highlights interesting aspects of genomic DNA methylation distribution in zebrafish, which are markedly different from mammals such as human and mice,” says lead author Aniruddha Chatterjee, from the Dunedin School of Medicine, the University of Otago, and Gravida: National Centre for Growth and Development.  “But we also show how this zebrafish methylome can be used to gain some fundamental mechanistic insights of DNA methylation biology (such as role of CpG island shore methylation, possible regulatory of distant CpG sites from genes).”

Take the dive into more methylome data at Epigenetics, September 2013.