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This Week in Genome Biology: Dec 30, 2015

A McGill University-led team explores genetic and environmental impact on human methylome variation in dozens of adipose tissue and blood samples from identical or non-identical twins. In an effort to characterize methylation patterns at sites with or without high levels of cytosine and guanine bases, the researchers did whole-genome bisulfite sequencing on adipose samples from seven pairs of identical twins, six non-identical twin pairs, and eight non-twin individuals. They used the same approach to test blood samples from the same twin pairs and one singleton. Results from the analysis helped to define the typical distribution of methylated sites in the genome as well as sites that vary depending on genetic or non-genetic factors such as tobacco smoking.

Researchers from the KTH Royal Institute of Technology in Sweden and elsewhere describe microbial community features that tend to be found in brackish water samples from the Baltic Sea. Using a combination of metagenomic sequencing, sequence binning, and phylogenetic analyses, the team assessed more than three-dozen samples collected in the Baltic Sea between March 2012 and December 2012. The approach produced 83 meta-genome assembled genomes, representing new and known representatives from the Actinobacteria, Bateroidetes, and several other diverse microbial phyla. From comparisons with metagenomic data described for other bodies of water, meanwhile, the study's authors saw signs of "a global brackish meta-community whose populations diverged from freshwater and marine relative over 100,000 years ago."

Finally, through deep genome sequencing on a Namibian cheetah named Chewbaaka and resequencing on half a dozen other cheetahs from Namibia or Tansania, an international research team got a look at the evolutionary history and current genetic diversity of the African cheetah, Acinonyx jubatus. As they report in Genome Biology, the researchers saw signs of at least two main population bottlenecks in the African cheetah — occurring 12,000 and 100,000 years ago — that have contributed to the decreased genetic diversity found in the endangered cats. GenomeWeb has more on the study, here.

The Scan

RNA Editing in Octopuses Seems to Help Acclimation to Shifts in Water Temperature

A paper in Cell reports that octopuses use RNA editing to help them adjust to different water temperatures.

Topical Compound to Block EGFR Inhibitors May Ease Skin Toxicities, Study Finds

A topical treatment described in Science Translational Medicine may limit skin toxicities seen with EGFR inhibitor therapy.

Dozen Genetic Loci Linked to Preeclampsia Risk in New GWAS

An analysis of genome-wide association study data in JAMA Cardiology finds genetic loci linked to preeclampsia that have ties to blood pressure.

Cancer Survival Linked to Mutational Burden in Pan-Cancer Analysis

A pan-cancer paper appearing in JCO Precision Oncology suggests tumor mutation patterns provide clues for predicting cancer survival that are independent of other prognostic factors.