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.