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Exploring the dark matter of the genome

tion to the next."

Says Smith, "The heterochromatin is where transposons may be actively regulated -- they go in, get stuck, and get chopped up. Other researchers have shown that small interfering RNAs are made in the heterochromatin, which seek out transposons and inactivate them. That's the kind of knowledge that comes from sequencing heterochromatin."

Smith uses the metaphor of dark matter to suggest the significance of heterochromatin. "We don't know what holds the galaxies together, and the same is true of the genome. We're pretty good at understanding how individual genes work, but we don't understand, for example, how the large-scale structure of genomes affects cellular processes. We hear too much about the 'post-genomic era' -- it's underappreciated that we don't understand the genome yet."

Celniker agrees. "What we would like to see is a complete sequence of the fruit fly from telomere to telomere" -- that is, from one end of the chromosomes to the other -- including the centromere in the middle." Obtaining a more complete picture of the sequence of heterochromatin is clearly a crucial step toward a better understanding of genome functions.

Karpen notes that one intensively studied and puzzling problem in chromosome biology will benefit enormously from the new findings: epigenetics -- the inheritance of traits and genetic information as controlled by proteins associated with the chromosomes, rather than by DNA sequence. Starting in the 1920s, epigenetics was discovered through biological studies of heterochromatin, and is now known to regulate essential functions such as those of the centromeres. The heterochromatin sequence of Drosophila will provide an essential foundation for identifying the proteins and components involved in epigenetic inheritance, as well as other mysteries surrounding the genome's "dark matter."

"Sequence finishing and mapping of Drosophila melanogaster heterochromatin," by
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Source:DOE/Lawrence Berkeley National Laboratory


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