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UD research featured in three academic journals

Blake C. Meyers

NEWARK, DE.--Groundbreaking plant genome research being conducted by the University of Delaware’s Blake C. Meyers has been featured in three academic journals in the last three months.

Work by Meyers, an assistant professor of plant and soil sciences who is affiliated with both UD’s College of Agriculture and Natural Resources and the Delaware Biotechnology Institute, and his research group was featured in the June issue of Plant Physiology and in the August issues of Nature Biotechnology and Genome Research.

The research centers on the transcriptional and genomic analysis of the model plant Arabidopsis using Lynx Therapeutics’ transcriptional profiling technology called Massively Parallel Signature Sequencing, or MPSS, to characterize diversity and expression patterns. Data is then posted to a public web site at [http://mpss.udel.edu/at/].

Meyers’ laboratory provides tissue samples to Lynx, which sequences short “signatures” from each of millions of ribonucleic acid (RNA) molecules. When Lynx has completed this transcriptional profiling, they return the results to the UD research team for analysis.

One of the unique aspects of the technology, Meyers said, is that it allows the identification and measurement of nearly all expressed genes in a particular tissue.

The article in Plant Physiology concerned the web site itself, which Meyers said has proven to be a “quite a popular page.” The Nature Biotechnology article was about the biological findings that came out of the research, and Genome Research reports on the methodology, or the bioinformatics, what Meyers called “the gritty details of our approach.”

Meyers said he was gratified to have three papers in quick succession in three different scientific journals. Publication of the Genome Research and Nature Biotechnology papers was specifically timed to coincide so that readers would be able to compare simultaneously the methods and findings.

In Genome Research, Meyers and his co-authors described how the research team works with the data gleaned through MPSS. His is the first laboratory to work with this data in the public domain, and he discussed the novel approaches the group has developed. He also included the first critical assessment of data produced by the technology.

In Nature Biotechnology, Meyers and his coauthors discussed the transcriptional and genomic analysis of Arabidopsis. His laboratory has developed five libraries of data based on information gleaned from different plant tissues. For interpretation, these data were compared with the genomic sequence information that has been produced by an international consortium over the last five to 10 years.

“With the five libraries, we wanted to compare data to determine what we can tell about the genomic sequence that was not known before,” Meyers said.

What they have found in the MPSS sequence information is that there are “many signatures that map to locations in the genome where no genes were expected,” he said, and “that tells us there are potentially many more transcripts than had been predicted.”

RNA is the only biological polymer that can both act as a catalyst, in the manner of proteins, and store key information, like deoxyribonucleic acid (DNA). As such, it plays a key role in the life of cells.

Meyers said that one of the most unusual findings that came out of the application of this scientific approach is that the MPSS data indicate the presence of a large number of novel types of RNA transcripts. These may be regulatory or potentially non-coding RNA molecules that have not been previous predicted or observed.

Two more papers derived from Meyers’ work with the MPSS technology or data were also featured in the June issue of Plant Physiology, and a sixth paper will be published soon in the journal Molecular Biology and Evolution. This work was performed in collaboration with research groups in Germany and Scotland. Meyers said that the information provides an extremely rich source of data that can be used to study numerous aspects of gene expression on a whole-genome level.

Article by Neil Thomas
Photo by Kathy F. Atkinson