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Exploring the dark matter of the genome

many reasons, and especially for studying heterochromatin," says Susan Celniker, a scientist in Berkeley Lab's Life Sciences Division and a longtime member of the Berkeley Drosophila Genome Project (BDGP). "Over a third of the total DNA in a fruit fly is heterochromatin. The female fly has an estimated 60 megabases of heterochromatin" -- a megabase (Mb) is a million bases, the nucleotide building blocks of DNA -- "and the male has an estimated 100 Mb, because the Y chromosome, estimated at 40 Mb, is all heterochromatin."

Heterochromatin is concentrated in the chromosome's centromeres and telomeres. In a typically bow-tie-shaped chromosome, the centromere is the knot. Centromeres play a crucial role in controlling chromosome duplication during cell division. Telomeres are a chromosome's end-caps; they help prevent the accumulation of genomic damage.

Both heterochromatin and euchromatin are sequenced using a method called whole-genome shotgun sequencing. Celniker says, "We grind up whole flies and produce libraries of DNA fragments of two sizes, some that are 2 kilobases long" -- a kilobase (Kb) is 1,000 bases -- "and some that are 10 kilobases long. Contiguous lengths of sequence are assembled by matching overlaps of these fragments. With euchromatin, large, single-copy fragments practically assemble themselves, but it's harder to know how shorter pieces with many repeating sequences, typical of heterochromatin, fit together."

Thus the first "substantially complete" genome sequence of Drosophila, published in Science in March, 2000 by the Berkeley Drosophila Genome Project and Celera Genomics, was actually far from complete. It left out a third or more of the genome by covering only the fly's euchromatin and almost none of its heterochromatin.

Says Celniker, "First we devoted our efforts towards finishing the euchromatin, leaving the part of the sequence rich in repeats, the centromeric and telomeric regions, until later.
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Source:DOE/Lawrence Berkeley National Laboratory


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