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Scientific American: The 1 Percent Genome Solution
multiple ways that are described, along with the results, in a Nature
paper published online today and in a special issue of Genome
Research.
A major part of the project was identifying sequences that cells copy,
or transcribe, into RNA molecules. Cells make proteins from RNA they
copy from genes, but some RNAs play roles by themselves. In
addition, some studies have found evidence that species from flies
and worms to humans copy large amounts of RNA from noncoding
DNA, with no apparent purpose. Nevertheless, "before ENCODE, I
think a lot of people were skeptical of how real intergenic activity was,"
says bioinformatician and consortium member Mark Gerstein of Yale
University.
Although genes make up only 3 percent of the ENCODE sequence,
the consortium found that 93 percent of the sequence is transcribed.
Some of the transcripts hail from noncoding DNA, the researchers
report, but those that do match up with the 399 ENCODE genes
overlap with each other extensively.
Transcripts from 65 percent of the genes incorporate pieces of DNA
from relatively far outside of the genes or even from one or two other
genes, says molecular biologist and consortium member Tom
Gingeras of Affymetrix, a genome technology company in Santa
Clara, Calif. Researchers know that cells chop single genes into
shorter pieces called exons, which they mix and match into one
transcript for creating a protein. Gingeras says the ENCODE findings
confirm recent reports that humans and flies sometimes combine
exons from two different genes.
Based on the transcript sequences, the researchers identified 1,437
new promoters—short DNA sequences where transcription begins—in
or between genes, on top of the 1,730 promoters they knew of. That is
nearly ten promoters per gene, Birney says. He adds that the
abundance of transcripts that overlap each gene suggests that the
very term "gene" should mean something different inside the cell
nucleus, where transcription takes place, than outside of it, where
finished proteins go.
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http://www.sciam.com/print_version.cfm?articleID=278A0C88-E7F2-99DF-32631...
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6/15/2007