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Team Tracks Epigenomic Diversity in Arabidopsis

NEW YORK (GenomeWeb News) – An effort to characterize epigenetic patterns and their interactions with underlying genetic profiles in the model plant Arabidopsis thaliana highlights the epigenetic variation present in plant populations.

As they reported online today in Nature, researchers from Salk Institute, the University of California, San Diego, and elsewhere performed genome, transcriptome, and/or methylome sequencing on hundreds of wild Arabidopsis thaliana plants from a range of climates and geographic locales in the Northern Hemisphere.

In parsing this data, the group considered everything from the presence of so-called single methylation polymorphisms, or SMPs, within specific sequence contexts to relationships between epigenetic profiles and DNA variants. Together, this information pointed to previously unappreciated levels of epigenomic variability within and between Arabidopsis populations.

"We looked at plants collected from around the world and found that their epigenomes are surprisingly different," Salk Institute plant biologist Joseph Ecker, the study's corresponding author and a Salk international council chair in genetics, said in a statement.

"This additional diversity may create a way for plants to rapidly adapt to diverse environments without any genetic change in their DNA, which takes a very long time," Ecker added.

By better understanding such epigenetic adaptation and its roots, researchers are optimistic that they will gain a better understanding of plant biology and, perhaps, hints as to how they might harness or tweak certain epigenetic marks — for instance, at sites in the genome where methylation is used to maintain gene silencing.

"Understanding how these methylation variants form in the wild will help toward better engineering of epigenomes," said co-lead author Matthew Schultz, a graduate student in Ecker's lab.

In a statement, Schultz said that by determining when and how genes are silenced by methylation marks, it may eventually become possible to selectively reactivate some of the methylation-muted genes.

Prior studies suggest that DNA methylation tends to occur at places in plant genomes where cytosine bases are either directly followed by guanine (CG-methylation) or by one of the other three bases and then by guanine (CHG-methylation). Methylation may also affect cytosines that precede two non-guanine bases in a row, researchers said, which is known as "CHH" methylation.

Some sites in the plant genome are also subject to a form of methylation mediated by RNA, they noted. But questions remain about methylation patterns across plant populations and within the CG-, CHG, and CHH- sequence contexts, with some sites seemingly showing epigenetic variation that is independent of genetic variation and others sharing ties to nearby DNA variants.

For their new study, the researchers sequenced the genomes of 217 A. thaliana plants collected throughout the Northern Hemisphere. They also did RNA sequencing on nearly 150 plants and turned to a MethylC-Seq approach similar to that described by Ecker and colleagues in the past to sequence the methylomes of 152 A. thaliana plants.

"Integration of genomic and epigenomics data allowed investigation into variable methylation states of both CG gene-body methylation and loci targeted by [RNA-directed DNA methylation]," the study authors said, "along with their interactions with genetic variants at the population level."

When they began diving into this data, for instance, investigators identified hundreds of thousands of apparent SMPs — on the order of 92,646 SMPs to 527,393 SMPs per A. thaliana accession. These epigenetic variants are somewhat akin to SNPs in DNA sequences, they explained, but seem to arise more rapidly than genetic changes.

Phylogenetic analyses built around the epigenomic variants resembled a genomics-based Arabidopsis phylogeny when the team considered SMPs in the CG sequence context. But fewer features were shared between SNP- and SMP-focused phylogenies in the case of SMPs at CHG-methylated or CHH-methylated sites.

Sequence context seemed to play a part in other epigenomic patterns, too, from the tendency of a given site to be methylated or unmethylated in specific parts of the genome to its propensity for differential methylation between plant populations.

By bringing together their epigenomic, genomic, and transcriptomic data, meanwhile, authors of the study also got a peek at potential interconnections between gene expression, variation at the methylation level, and DNA sequence or structural variants.

Through association mapping, for example, the team detected genetic loci that appear to influence spots in the Arabidopsis genome that are prone to differential methylation. It also learned more about the process of RNA-directed methylation and the types of genes that tend to be targeted by it.

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