In a PLoS One paper published this week, investigators at the King Abdullah University of Science and Technology in Saudi Arabia present the Dragon Database of Polymorphic Regulation of miRNA genes, or dPORE-miRNA, which aims to "facilitate the investigation of the potential effects of single nucleotide polymorphisms on miRNA gene regulation." The dPORE-miRNA database incorporates transcription factor binding site data and is freely accessible here and here.
Also in PLoS One this week, Utah State University's Kenneth Locey and Ethan White report their use of "randomization tests based on Morisita's Index of aggregation to examine average differences in the distribution of purines and pyrimidines among coding and non-coding" DNA from 223 microbial genomes. "Purines and pyrimidines were aggregated in the non-coding DNA of 86 percent of genomes, but were only aggregated in the coding regions of 52 percent of genomes," Locey and White report, adding their observation that "genome length appears to limit aggregation, but chromosome length does not."
Over in PLoS Genetics, researchers at the University of Southern California show that "nucleosomes containing methylated DNA stabilize DNA methyltransferases 3a/3b and ensure faithful epigenetic inheritance." More specifically, such nucleosomes permit few free DNMT3A/3B enzymes to exist in the nucleus, the authors show, adding that this observed "stabilization of DNMT3A/3B on nucleosomes in methylated regions further promotes propagation of DNA methylation" in an apparent, unexpected self-regulatory mechanism.
A collaboration among researchers at the Australian Wine Research Institute in Adelaide and 454 Life Sciences in the US reports its comparison of whole-genome assemblies for six commercial Saccharomyces cerevisiae strains, some of which are used in brewing. The team found that each strain is defined by "clear signatures" for each industrial S. cerevisiae class, comprised of SNPs as well as large-scale insertions and deletions.