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Genomics In The Journals: Oct 18, 2012

NEW YORK (GenomeWeb News) – In Nature Genetics, a research team from Israel has reported on DNA methylation dynamics at sites in the genome where the epigenetic mark occurs at variable levels.

The researchers first highlighted the presence of these epigenetic polymorphisms, nicknamed epipolymorphisms, in populations of normal and cancerous cells — an analysis that hinged on bisulfite sequencing-based methylation data generated for past studies. They then used sequencing- and array-based methods to follow methylation patterns in two immortalized fibroblast cell lines undergoing somatic cell evolution over hundreds of generations in the lab. Within each population of cells, their results suggested that average methylation levels at a given genomic locale can jump or subside when susceptibility to methylation at that site shifts in a significant proportion of cells that make up that population.

"We hypothesize that resistance mechanisms mask DNA from otherwise pervasive and locally random events of methylation aberration," Weizmann Institute of Science researcher Amos Tanay, the study's senior author, and colleagues wrote, "and that gain or loss of such resistance may be instrumental in the emergence of tissue- and cancer-specific epigenomic patterns."

Researchers from Switzerland, Indonesia, and the UK provide a peek at the population structure and migratory patterns of Sumatran orangutans in the Journal of Heredity.

The group assessed mitochondrial hyper-variable region I sequences in 123 Sumatran orangutans and autosomal microsatellite repeat markers in 109 more animals using DNA isolated from wild orangutan hair and stool samples. For a few captive, wild-born orangutans, researchers also had access to blood samples.

The study uncovered an unexpectedly high level of genetic diversity in an orangutan group living on the Indonesian island's west coast, indicating that the 400 or so orangutans found there today are descended from a much larger population that once made its home in the area. Results from the broader genetic analysis point to population structure amongst the Sumatran orangutan groups, likely reflecting their geographic isolation from one another. But the team also saw signs that some male orangutans can travel long distances to breed with other populations.

"This result highlights the need to conserve … important dispersal corridors to uphold genetic exchange," University of Zurich Anthropological Institute & Museum researcher Alexander Nater, the study's corresponding author, said in a statement, "and it also gives hope that it is not yet too late to preserve these unique Asian great apes."

Regions of the honey bee genome known to be rife with recombination contain genes that are preferentially expressed by bees in the worker caste, potentially influencing the behavior of these bees, according to a study by York University researchers in the early, online edition of the Proceedings of the National Academy of Sciences.

In an effort to understand if, and how, heterogeneous features of the honey bee genome influence the insect's social traits, investigators stepped back to find the ancestral forms of polymorphisms in the honey bee genome — a feat accomplished through comparisons of the honey bee genome and sequences of other species from the same genus. Results of that analysis and others indicated that parts of the honey bee genome that are particularly rich in cytosine and guanine nucleotides have arisen — and been maintained — through processes that include recombination and biased gene conversion. These GC-rich, recombination-prone parts of the genome are not only genetically diverse, researchers reported, but are also home to worker bee-expressed genes linked to characteristic behaviors in that bee caste.

"The honey bee has the highest rates of recombination in animals — 10 times higher than humans," first author Clement Kent, a post-doctoral researcher in senior author Amro Zayed's York University genetics and genomics lab, said in a statement. "Our study shows that this high degree of genetic shuffling has turned on the evolutionary faucet in parts of the bee genome responsible for orchestrating worker behavior."

"This can allow natural selection to increase the fitness of honey bee colonies, which live or die based on how well their workers 'behave,'" Kent added.

Researchers from Saudi Arabia and the Netherlands describe in the New England Journal of Medicine the strategy they used to hunt down a previously undescribed coronavirus that appears to have caused a fatal infection in a 60-year-old Saudi Arabian man.

The patient, who was admitted to the hospital with an unexplained case of acute pneumonia, went on to develop kidney failure and eventually succumbed to the disease. After ruling out the usual infection suspects, investigators turned to PCR-based assays to look for new viruses in the patient's sputum samples, identifying a coronavirus that was subsequently sequenced using Roche 454 and Sanger approaches.

The virus, dubbed HCoV-EMC, is most closely related to two bat-infecting coronaviruses, they explained. And the condition it produced shared clinical features with those described during a 2003 outbreak of severe acute respiratory syndrome that was caused by another coronavirus, SARS-CoV.

"This case is a reminder that although most infections with human coronaviruses are mild and associated with common colds, certain animal and human coronaviruses may cause severe and sometimes fatal infections in humans," Erasmus Medical Center's Ron Fouchier, the study's senior author, and colleagues concluded.

"Although HCoV-EMC does not have many of the worrisome characteristics of SARS-CoV," they added, "we should take notice of the valuable lesson learned during the 2003 SARS outbreak with respect to outbreak investigations and management."

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

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