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Exploring the dark matter of the genome

latively easy to perform in euchromatin but harder in heterochromatin, "because it is so rich in repeats."

Smith and his colleagues found evidence for 230 to 254 protein-coding genes in the heterochromatin, previously thought to contain a mere 30 to 40 (the fly's total is 14,000 or more). Many of these genes were organized quite differently from genes in euchromatin, with much longer gaps (introns) between the coding sections of the gene (exons); unlike the introns in euchromatic genes, these long gaps consisted almost entirely of repeating sequences derived from disabled transposons. The evidence suggests that heterochromatic genes are regulated differently from euchromatic ones.

Besides protein-coding genes, the annotators found other significant elements in the heterochromatin, including 13 single-copy genes that do not code for proteins but for small RNA structures called noncoding RNAs.

They also found pseudogenes -- truncated copies of genes which have become inactive, most likely because they have been duplicated or code for traits no longer needed by the organism. Drosophila has very few pseudogenes compared to most complex organisms (humans have some 20,000), but the annotators found 32 new ones in the heterochromatin, more than twice as many as previously described.

Finally, the annotators calculated the kind and distribution of repeating elements. "The heterochromatin is incredibly repeat-rich," says Smith, "and most of it is transposable elements that have been chewed up and fragmented."

Susan Celniker emphasizes that transposable elements, of which 96 families have been found in Drosophila so far, "can be very dangerous. They are viruses -- literally." She points out that during subsequent sequencing efforts, DNA was made three times from the same strain of flies -- in 1990, 1998, and 1999 -- and that new patterns of transposons were found in each. "We can see intact transposons moving from one posi

Source:DOE/Lawrence Berkeley National Laboratory

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