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This Week in PLoS : Nov 21, 2011

In PLoS Computational Biology this week, Sun Yat-Sen University's Zhiming Dai and Xianhua Dai show that "gene expression divergence is coupled to evolution of DNA structure in coding regions." More specifically, the duo reports its investigation of "the contribution of DNA three-dimensional structural evolution as cis to gene expression divergence" in yeast, in which it found that the two are correlated. The team observed a similar correlation among Drosophila species. "These results reveal the previously unappreciated roles of DNA structure as cis-effects in gene expression," the authors write.

Elsewhere in the journal, researchers at the Los Alamos National Laboratory in New Mexico show that "imposing gene start consistency improves the accuracy of gene start-site prediction." Using an algorithm that employs a genome majority vote scheme on a set of validated E. coli genes, the team found it could "correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors." The Los Alamos team says its approach lends additional accuracy to gene map production.

Over in PLoS One, a team led by investigators at Xi'an Jiaotong University shows in a Chinese population that six SNPs in the obesity-associated FTO gene are also significantly associated with hip bone mineral density. "These six SNPs are all located at the intron 8 of FTO and in high linkage disequilibrium," the authors write. The team adds that none of those SNPs showed significant associtation with bone mineral density in a Caucasian sample, however.

And in PLoS Genetics this week, the University of Minnesota's Nathan Springer and his colleagues provide "evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences." The team adds that "the epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance."

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.