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Objection #2: Why Sequence the Junk?

Science  16 Feb 2001:
Vol. 291, Issue 5507, pp. 1184
DOI: 10.1126/science.291.5507.1184

Genes and their corresponding proteins get most of the attention, but they make up only a tiny fraction—1.5% or less—of the human genome. The other 98% of DNA sequence that does not code directly for proteins was once dismissed as “junk DNA,” and numerous researchers argued that it would be a waste of time and money to include the repetitive, hard-to-sequence regions in the genome project. But scientists have discovered many riches hidden in the junk, and as the project nears completion, several researchers predict that some of the most intriguing discoveries may come from areas once written off as genetic wastelands.

Included among the noncoding DNA, for example, are the crucial promoter sequences, which control when a gene is turned on or off. The repetitive sequences at the ends of chromosomes, called telomeres, prevent the ends of the chromosome from fraying during cell division and help determine a cell's life-span. And several teams have begun to make a strong case that repetitive, noncoding sequences play a crucial role in X inactivation, the process by which one of the two X chromosomes in a female is turned off early in development. Other genes are turning up in areas previously dismissed as barren. Scientists had assumed, for example, that the regions next to telomeres were buffer zones with few important sequences. But in this week's issue of Nature, H. C. Reithman of the Wistar Institute in Philadelphia and his colleagues report that these regions contain hundreds of genes. “The term ‘junk DNA' is a reflection of our ignorance,” says Evan Eichler of Case Western Reserve University in Cleveland.

The human genome has much more noncoding DNA than any other animal sequenced so far. No one yet knows why. At least half of the noncoding DNA seems to be recognizable repeated sequences—perhaps genomic parasites that invaded the genomes of human ancestors. Eichler suspects that such repeats might provide some genomic wiggle room. Long stretches of noncoding DNA provide “a built-in plasticity that may be bad at the individual level, but if an organism is going to evolve, it may be a huge selective advantage,” he says.

“There is a rich record of our history” in the repeats, agrees Francis Collins of the National Human Genome Research Institute in Bethesda, Maryland. “It's like looking into our genome and finding a fossil record, seeing what came and went.”

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