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Genomics in the Journals: Aug 1, 2013

NEW YORK (GenomeWeb News) – In Genome Biology, researchers from the US, Russia, and France described a group of very long intergenic non-coding RNAs, or vlincRNAs, that have promoters found in parts of the human genome containing retroviral repeat sequences.

The group unearthed the retroviral element-related non-coding RNAs during a broader analysis of vlincRNAs. Using new and existing RNA sequence data from human primary cells and other normal or cancerous human tissues, it uncovered 2,147 vlincRNAs, together covering an estimated 10 percent of the human genome.

When they began looking at these vlincRNAs in more detail, the investigators saw that the RNAs are found in a wide range of human cell types, where they seem to make functional contributions.

In addition, they determined that many of the vlincRNAs with tissue-specific expression patterns had promoters falling in endogenous retroviral sequences — particularly those associated with long terminal repeats. The expression of vlincRNAs with retroviral promoters appeared to jump in cells marked by pluripotency or malignancy, too, prompting the study's authors to propose a "previously unknown connection between the pluripotent state and cancer via retroviral repeat-driven expression of vlincRNAs."

A DNA base change detection method outlined by University of Washington and Rice University researchers in Nature Chemistry is being touted as a potential tool for testing and treating conditions that involve a limited number of clinically informative single nucleotide swaps.

The approach uses conditionally fluorescent molecular probes — together with a hybridization step that relies on what that the team calls a "double-stranded toehold exchange mechanism" — to find individual base changes in a specific stretch of double-stranded DNA.

After trying out their variant detection strategy on synthetic double-stranded DNA, the study's authors took a crack at applying it to bacterial DNA from Escherichia coli. There, they reported, the method proved useful for seeing variants in the E. coli gene rpoB, including alterations expected to render the bug resistant to the drug rifampicin.

"The ability to identify single point mutations is critical for diagnosing antibiotic resistance in tuberculosis and other diseases," the study's authors noted, "because most drug resistance can be traced to individual point mutations in narrowly defined regions within a few genes."

"Our probes can be used to screen extended genetic regions (that potentially contain multiple SNPs in different positions)," they added, "and can be multiplexed to screen mutations that occur in different genes, which makes this a promising technology for developing rapid and reliable infectious disease diagnostics."

Researchers from Germany, the UK, and Belgium used genome sequencing to see Helicobacter pylori evolution and transmission patterns in two South African families — work that they described in the early edition of the Proceedings of the National Academy of Sciences. By sequencing 97 H. pylori isolates from 52 individuals belonging to two rural South African families, the team identified 45 family members who carried at least two different H. pylori strains.

In 40 of the individuals, the co-occurring H. pylori strains shared all but a few sequences with one another, making it possible for researchers to look at within-host evolution events such as mutation, recombination, and immune selection in more detail. In the other five individuals, sequence data suggested that coincident strains of stomach ulcer-causing bacteria were more distantly related — the apparent result of co-infection by different H. pylori strains in those individuals.

The sequence data helped the researchers start retracing H. pylori transmission events, too, both between individuals living under the same roof and across families as a whole. While transmission does seem to happen fairly frequently within families, they found, members of the same family were not always involved in transmission events. Likewise, more than half of those tested did not appear to have transmitted H. pylori to others.

A recurrent change to the kinase-coding gene PRKG1 can contribute to the development of serious conditions affecting the thoracic aorta, a vessel that moves blood from the heart to other parts of the body through the chest, according to a study in the American Journal of Human Genetics.

A large research team that included investigators from the National Heart, Lung, and Blood Grand Opportunity Exome Sequencing Project, the GenTAC Registry Consortium, and elsewhere did exome sequencing on two distantly related individuals from a large family affected by thoracic aortic aneurysms or by acute aortic dissections, a life-threatening complication that can develop from such aneurysms.

The search led to a rare, gain-of-function glitch in the type I cGMP-dependent protein kinase-coding gene PRKG1. Researchers subsequently detected the same PRKG1 alteration in members of three other thoracic aortic disease affected families using exome sequence data or targeted Sanger sequencing.

The team's follow-up analysis of the thoracic aortic disease-associated mutation in PRKG1 suggest that the alteration amps up the activity of the resulting PKG-1-alpha protein, causing changes in myosin protein phosphorylation in certain cells and a dip in vascular smooth muscle cell contractions.

"[I]dentification of a gain-of-function mutation in PRKG1 as a cause of thoracic aortic disease provides further evidence that proper [smooth muscle cell] contractile function is critical for maintaining the integrity of the thoracic aorta throughout a lifetime," corresponding author Dianna Milewicz, with the University of Texas Health Science Center at Houston, and her colleagues wrote.

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.