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This Week in Nature: Nov 18, 2010

In a paper published online in advance in Nature Genetics this week, researchers in China and Denmark describe genome-wide signatures of genetic diversity and selection in 17 wild and 14 cultivated soybean genomes, which they re-sequenced at an average depth of approximately 5x and more than 90 percent coverage. The wild soybean genomes, the team reports, show higher allelic diversity than the cultivated ones. The group also proposes a set of 205,614 single-nucleotide polymorphisms that "may be useful for [quantitative trait locus] mapping and association studies," the authors write.

Investigators in the UK and Germany show that ubiquitous overexpression of the Fto gene causes obesity in mice, irrespective of the animals’ diets. In addition, mice that lack Fto expression show a lean phenotype; those that overexpress Fto and consume high-fat diets develop glucose intolerance, the team shows in Nature Genetics this week.

The Whitehead Institute's David Bartel and his colleagues describe a high-throughput method to identify polyadenylated RNA termini – based on poly-A position profiling by sequencing -- which they used to identify 3'-untranslated regions in Caenorhabditis elegans. Using 3P-seq, Bartel et al. identified more than 8,500 additional 3’-UTRs in the nematode and found that "30 percent of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,480 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening." In addition, the Whitehead-led team shows that nematode 3'-UTRs – though they are, on average, about one-sixth the length of those in mammals – "have twice the density of conserved microRNA sites," the authors write.

And in another Nature paper published online this week, investigators at The Scripps Research Institute in La Jolla, Calif., along with their collaborators at the University of Washington show that "quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins." More specifically, using quantitative proteomics methods, the Scripps-led team profiled the reactivity of cysteine residues in biological systems. The team also suggests that quantitative reactivity profiling can discriminate between catalytically active and inactive cysteine hydrolases.

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.