Less is more: New technology captures gene-rich DNA segments

December 18, 2003

Obtaining genome sequence information frequently leads to breakthroughs in the study of a particular organism. Bringing agriculturally important plant species into the genomic age is therefore an important goal. However, because they are typically larger or much larger than the 3-billion letter human DNA sequence and have a high proportion of so-called repetitive DNA that is difficult to sequence and contains few coding regions or genes, the genomes of many plants--including most agriculturally important species--have posed significant challenges to researchers interested in crop improvement, plant molecular biology, or genome evolution. A new study by Cold Spring Harbor Laboratory researchers is a significant step toward overcoming those challenges.

By applying a method they recently developed that captures gene-rich regions and excludes the vast majority of repetitive, gene-poor DNA, Cold Spring Harbor researchers have now achieved a dramatic shortcut to sequencing the genes of corn. The approach should provide a similar boost to the sequencing and comparative analysis of other genomes in a wide variety of biological, biomedical, and biotechnological settings.

The study, led by Cold Spring Harbor Laboratory scientists W. Richard McCombie and Robert Martienssen, is published in the December 19 issue of Science along with a related study carried out by researchers at The Institute for Genomic Research in Rockville, Maryland. A key method used in both studies, called methylation filtration, was developed in 1999 by McCombie and Martienssen's groups through work funded by the U.S. Department of Agriculture.

Methylation filtration relies on the observation that the DNA of repetitive, gene-poor regions in the corn genome (and other plant genomes) is modified by a process called methylation, whose study has been pioneered in part by Martienssen's group. Methylation filtration takes advantage of this observation to preferentially capture the unmethylated, gene-rich regions of the corn genome for subsequent analysis. Indeed, the new study demonstrates that methylation filtration removes 93% of repetitive, gene-poor DNA. As a result, the researchers were able to focus their efforts on the sequencing and analysis of the gene-rich regions of the corn genome.

"This study establishes that methylation filtration, combined with other simple techniques, can be used to successfully recover and properly assemble complete gene sequences from genomes that are otherwise extraordinarily difficult to decipher," says McCombie. "Moreover, both studies involved large-scale tests that validated our initial estimates regarding how well the procedure would work. Perhaps most importantly, we've shown that after gene-enriched draft DNA sequences are obtained, they can be converted into the complete sequence of the corn genes by using the related, but much smaller rice genome sequence as a guide. We believe that taking this short-cut approach has brought us a very close to a final sequence map of the biologically important regions of the corn genome at a fraction of the cost of other approaches," adds McCombie.

The rice genome, which is about 1/6 the size of the corn genome, is being sequenced as part of an international consortium funded in the United States by the National Science Foundation and the U.S. Department of Agriculture. Corn is the most important agricultural crop in the U.S. Because the genome structures of wheat, oats, barley, and many other crops are quite similar to that of corn, the approaches outlined by the new study provide the means to bring investigations of all of these important crops into the genomics era.
The study was funded by the National Science Foundation Plant Genome Research Program (http://www.nsf.gov/bio/dbi/dbi_pgr.htm). Dr. Jane Silverthorne, Director of NSF's Plant Genome Research Program, says, "The success of this project highlights the importance of virtual center projects in bringing together the expertise required to tackle large complex problems in genomics."

To Contact the Principal Investigators on the Study:
W. Richard McCombie: mccombie@cshl.edu
Robert Martienssen: martiens@cshl.edu.

To Contact the National Science Foundation Plant Genome Research Program:
Jane Silverthorne (Program Director): jsilvert@nsf.gov

Cold Spring Harbor Laboratory

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