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Salk Team Gets Better Resolution, New Browser


You can't get much better resolution than the single-nucleotide level. Joe Ecker and his team at the Salk Institute report that they've done just that to look at the epigenome of Arabidopsis thaliana. "Our aim was to really go much further — previously, genome-wide analysis of genome methylation of Arabidopsis had used tiling microarrays — and really go to the ultimate resolution of DNA methylation," says Ryan Lister, a postdoc in Ecker's lab and first author on the Cell paper describing their work.

To study the epigenome, Lister and his colleagues sequenced the different levels of regulation of the Arabidopsis genome, including the methylation of cytosine, mRNA transcripts, and small RNA transcriptome. With a next-gen sequencer, they looked at those different aspects in a wild-type strain as well as three DNA methyltransferase or demethylase mutants. Methylation and demethylation of the genome is a dynamic process, says Lister, that keeps certain regions of the genome methylated and protects others from methylation. "You've got both patterns that appear to be quite stably inherited and passed on for cells and generations, and you've got areas of the genome which are being targeted and also protected from DNA methylation," he says.

To handle the amount of data needed to get to such a high level of coverage, Lister contacted a colleague from Australia to design a new genome browser tailored for this project. "We wanted a tool that would allow us to look at many different orders of magnitude of zooming in on the genome," Lister says. "It is really dynamic — with your mouse, just grab the data and move it around and really get your hands on it and do quality control checking of what your data looks like."

With all this information neatly organized, they were able to see that when DNA methylation levels changed, the abundance of hundreds of non-genes and intergenic transcripts also changed. They also found incorrectly annotated genes with novel exons as well as antisense transcripts. The team was able to study transcript families without fear of cross-hybridization. "That's the real advantage of sequencing," Lister says. "You know exactly what you've got. You've got the sequence of it. You know exactly where it originated from in the genome."

Lister, along with the rest of Ecker's lab, will continue to look at natural variation in DNA methylation by sequencing related strains of Arabidopsis to determine if these epigenetic changes are associated with genetic variation.

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