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Chicken genomic sequence yields insight into vertebrate evolution

e not present in the publicly available first draft of the chicken genome assembly.

"Forests" and "deserts": identifying functionally important elements in the genome

Distinguishing the genomic sequences with more mundane functions from those with biologically evident roles is one of the major challenges facing researchers in the field of genomics. Approximately 25% of the human genomic sequence is considered to be "gene deserts," or megabase-long spans of genomic DNA lacking protein-coding genes. Ivan Ovcharenko, Ph.D., a Bioinformatics Scientist at Lawrence Livermore National Laboratory, and his colleagues cooked up a computational recipe in their Genome Research contribution and classified "gene deserts" into two categories: stable and variable. The characterization of such regions is important for researchers looking for disease-causing mutations in genomic DNA, because studies such as this highlight large regions of the genome that are not likely to harbor such mutations. "There are many indications that stable gene deserts may represent treasure boxes of multiple gene regulatory elements," says Ovcharenko, "while the variable gene deserts may be depleted in biological activity."

In contrast to gene-deficient regions of the genome, the identification of "gene forests" has been aided by work such as that by Stuart Wilson, Ph.D., from the Department of Molecular Biology at University of Sheffield in the U.K. In their Genome Research publication, Wilson and his colleagues characterized the chicken transcriptome, or the RNA molecules that are encoded by the genes in the chicken sequence. These transcripts form the basis for many downstream biological processes, and their characterization is important for basic biological studies in the chicken, including those in embryology, development and disease. Wilson's website (www.chick.umist.ac.uk), produced as a result of
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Contact: Maria A. Smit
smit@cshl.edu
516-422-4013
Cold Spring Harbor Laboratory
8-Dec-2004


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