In PLOS Genetics, researchers from Cornell University, Elon University, and Weill Cornell Medical College explore the regulatory features under selective pressure in vertebrate genomes, particularly microRNAs and the sequences they target. Using nucleotide substation event simulations and available vertebrate genome sequences, the team searched for signs of selection on miRNA targets, identifying a handful of distinct evolutionary patterns that affect the 3' UTR sequences targeted by deeply conserved, "ancient" miRNAs. "We find that mutations that strengthen or weaken existing target sites are strongly disfavored," the investigators write, noting that "even recently evolved target sites [of ancient miRNAs] are under strong selective constraint, and as miRNAs age, they tend to initially experience selection only against loss of existing target sites, and later accumulate strong selection against gain of novel target sites."
A team from China takes a look at the possibility of using human papillomavirus (HPV) sequences in the blood as a marker for cervical cancer. As they report in PLOS One, the researchers did a meta-analysis that included 684 cervical cancer patients profiled for more than a dozen past studies, focusing on circulating cell-free DNA stemming from HPV. Their results suggest that circulating HPV coincides with cervical cancer and may be a promising marker for diagnosing or following the trajectory of the disease. "Our meta-analysis suggested that detection of HPV [circulating DNA] in patients with cervical cancer could be used as a non-invasive early dynamic biomarker of tumors, with high specificity and moderate sensitivity," the authors write.
Researchers from Saudi Arabia and the US consider potential ties between obesity and salt sensitivity genes for another PLOS One paper. Starting with array-based gene expression data for visceral adipose samples from 16 overweight and 14 lean adolescent females, the team put together networks of genes that are co-expressed with salt sensitivity genes or interact with the proteins they encode. From the thousands of differentially expressed genes and interactions in the salt sensitivity network, the authors narrowed in on 16 interaction hubs and nearly two dozen salt sensitivity genes that appear to be enriched in the adipose tissue overall, along with genes and interactions that may be altered in samples from overweight study participants. Based on these and other results, they suggest that salt sensitivity genes "could act as molecular signatures for tracing the basis of adipogenesis among obese patients."