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This Week in Genome Research: Dec 9, 2009

In Genome Research this week, scientists led by the Netherlands Cancer Institute's Bas van Steensel and University of California, San Diego's Trey Ideker have created a network model of interacting chromatin proteins in the fruit fly genome. Basing their Bayesian model on genome-wide binding maps, they targeted a set of 43 chromatin components in Drosophila and found "many novel functional relationships," including that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner, they say in the abstract.

In other research, scientists at Duke University studied the origin recognition complex (ORC), a conserved complex of DNA binding proteins that initiates replication, in Drosophila. Looking at genome-wide binding of ORC, they found that "ORC localizes to specific chromosomal locations in the absence of any discernible simple motif," they write. "Open chromatin appears to be the underlying factor that is deterministic for ORC binding." Also, they found that often where ORC binds, cohesin loads, suggesting a role for ORC in the loading of cohesin on DNA.

To better understand the function of olfactory receptor (OR) genes across mammalian species, University College Dublin and Texas A&M University researchers compared them from 50 mammalian genomes. By amplifying more than 2,000 OR genes in aquatic, semi-aquatic, and flying mammals and combining this information with existing data on 48,000 OR genes from terrestrial mammals, they found that "functional OR gene repertoires were reduced independently in the multiple origins of aquatic mammals and were significantly divergent in bats," suggesting that ecological adaptation plays an important role in the evolution of OR gene families.

In work appearing in this month's issue of GR, Jason Lieb at the University of North Carolina, Chapel Hill, and team have developed a method called FAIRE, or formaldehyde-assisted isolation of regulatory elements, to map open chromatin during the mitosis-to-meiosis transition in S. cerevisiae. They found that open chromatin is associated with double-strand break hotspots and that this is most visible 3 hours into meiosis. They also saw that meiosis-induced chromatin opening happens at regions adjacent to boundaries of subtelomeric sequences.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.