Stanford geneticists, with two other California research teams, have characterized almost a third of active genes in a common research plant, enhancing a multinational genetic library that could help growers control plant characteristics from cold tolerance to flower color.

Stanford, UC-Berkeley and Salk Institute collaborators used two complementary methods to search the entire genome of the model plant Arabidopsis for areas of active transcription — the first step from a gene towards its protein end-product.

"This work is important for two reasons," said Audrey Southwick, PhD, of the Stanford Genome Technology Center. "First, it represents a huge effort in looking at how nature creates these transcripts, what they really look like. Second is the whole genome picture — not just limiting ourselves to what we know, but asking ‘what all is there?’

"On average in tissues we looked at, about 65 percent of the genome is being actively transcribed at a given time," said Southwick, who is co-author of the study, published recently in the journal Science. "The paper looks at what overlaps or is unique in different tissues."

The three teams were led by Ronald Davis, PhD, professor of biochemistry and of genetics and director of the Stanford Genome Technology Center; Sakis Theologis, PhD, of UC-Berkeley’s and the U.S. Department of Agriculture’s Plant Gene Expression Center; and Joseph Ecker, PhD, professor of biology at the Salk Institute.

Arabidopsi, or mouse-ear cress, is the geneticist’s user manual for flowering plants. This small, fast-growing plant has become a standard reference tool because it is easy to grow and has a relatively small genome — between 110 and 120 million DNA letter pairs, compared with the human genome’s 3 billion.

The DNA sequences of its five chromosomes are well-understood, and stocks of mutant Arabidopsis plants are available for research into the effects of gene variation on disease resistance, fruit production and more.

The plant’s DNA was sequenced in 2000, but the location of functional genes within that sequence was a matter of educated guesswork and computer modeling.

The holy grail of genetic research is not the genome itself, but the protein machinery built following its DNA instructions. Proteins do the real legwork in all living things — from digesting food to detecting sunlight. To find which proteins are being made, geneticists must scan the cell’s genetic alphabet soup and separate the words from the random strings. Then they must discover which words are actually part of the instructions, written in RNA that translates DNA words into proteins.

Davis, co-discoverer of the proteins that cut and splice DNA for genetic engineering, helped develop the whole-genome array technology that detected active genes in Arabidopsis.

The whole-genome array method uses a grid of plant DNA sequences, grown on a silicon microchip. RNA from plant tissue is poured over the chip. Each RNA strand sticks to the DNA word that it was made from. Special, light-reactive substances attached to the RNA light up, or fluoresce, under laser light — revealing where DNA words appear in the genome. "For the first time in plant biology, we have the whole genome sequence laid down, so we can do very global analysis of the genome," said Theologis.

"What’s unique about this type of array is that it lets you look at gene structure, more than just simple expression — whether the gene is on or off," Southwick said. "You can look at much more critical questions of regulation: Is this exon or intron different, where does the transcript start and stop?"

To confirm genes identified using the arrays, the team created and sequenced complementary DNA for the RNA they found. Using the combined methods, they discovered 6,000 new functional genes, according to Theologis. Half of the 6,000 were previously identified, but had been thought inactive. The other 3,000 were completely new.

Now that the new genes are identified, researchers can begin studying what proteins they encode, and what functions they perform in plants. Without the whole-gene array, finding a new gene can take months or years.

"On the whole-genome scale, we aren’t just limiting ourselves to what we already know," said Southwick. "There was all this other activity detected that wasn’t necessarily being looked for. This is a great opportunity for discovery."