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Exploring the dark matter of the genome

Not so long ago, the difficult-to-sequence, highly repetitive, gene-poor DNA found in regions of chromosomes known as heterochromatin was called "junk." Like dark matter in the universe, the true nature of heterochromatin was unknown.

Now members of the Drosophila Heterochromatin Genome Project (DHGP), headed by Gary Karpen of the Department of Energy's Lawrence Berkeley National Laboratory, are approaching a complete assembly, mapping, and functional analysis of those portions (other than simple repeats) of the heterochromatic DNA of Drosophila melanogaster, the fruit fly. The results confirm that heterochromatin is far from mere junk.

"Most researchers thought heterochromatin had little or no function, because it appeared to lack the protein-coding genes that occur so richly in the chromosomes' more accessible and better-studied euchromatin," says Karpen, a senior scientist in Berkeley Lab's Life Sciences Division and an adjunct professor of cell and molecular biology at the University of California at Berkeley. "In recent years it has become apparent that heterochromatin is critical for many essential functions."

Advances in sequencing the Drosophila heterochromatin have overcome previous technical limitations, extended understanding of heterochromatin's organization and constitution, and led to new insight into how it helps cells and organisms survive. The latest results from the DHGP are reported in a pair of papers in the June 15, 2007 issue of Science.

The annotated heterochromatic sequences reveal over 200 protein-coding genes. The heterochromatin also includes other features of biological importance, including sequences that code for non-protein-coding RNAs and other functional elements, such as small RNAs that neutralize transposable elements, or transposons -- DNAs similar to viruses that hop around the genome and are capable of disrupting gene function.

"Drosophila is ideal for studying genomics for
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Source:DOE/Lawrence Berkeley National Laboratory


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