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Genomics In The Journals: Nov 23, 2011

NEW YORK (GenomeWeb News) – A Chinese research team has identified mutations in the gene PRRT2 that are associated with a movement disorder known as paroxysmal kinesigenic dyskinesia, findings they describe online in Nature Genetics. The group found the truncating PRRT2 mutations by sequencing the exomes of two Han Chinese individuals with paroxysmal kinesigenic dyskinesia and two unaffected members of the same family. After narrowing the list of variants detected in the exomes based on predicted functional effects and their presence in affected versus unaffected individuals, the researchers focused on three genetic changes found in a chromosome 16 region detected in past dyskinesia linkage studies. One of these — a frameshift-causing indel in PRRT2 — was subsequently verified by Sanger sequencing and shown to co-segregate with the condition. Researchers found even more mutations that abbreviated PRRT2 when they screened seven other paroxysmal kinesigenic dyskinesia-affected families.

In BMC Evolutionary Biology, researchers from the US and France outline the strategy used to find more than a dozen previously unknown Caenorhabditis species. The team tracked down 16 new Caenorhabditis species by testing rotten fruit, flower, and stem samples from around the world. They then looked at the relationships between all 26 new and known Caenorhabditis species, including the lab model C. elegans, using a phylogenetic analysis based on a handful of protein-coding genes and a pair of rRNA genes. From genetic patterns and other traits, researchers defined two clades within Caenorhabditis, looked at geographic distribution patterns for the species, defined a barcode sequence for distinguishing between Caenorhabditis species, and began exploring the evolutionary history of the nematode worms.

"Using our new data we were able to generate an evolutionary tree for all 26 species which showed that the history of Caenorhabditis has had many evolutionary reversals and convergences," co-first author Karin Kiontke, a biology researcher at New York University, said in a statement. "The newly discovered species will be an important resource for future research and will doubtless teach us much more about the evolution of genomes, reproductive modes, and development."

A study in the early, online edition of the Proceedings of the National Academy of Sciences traces expression patterns in the human cytomegalovirus during the process of active infection. A UK research group did deep transcriptome sequencing on HCMV from human cell lines that had been infected with the virus for several days. Along with new protein-coding genes, the researchers detected extensive RNA splicing and a slew of non-coding RNA transcripts in HCMV's transcriptome. Most of these non-coding RNAs had been transcribed from parts of the HCMV genome that don't overlap with protein-coding sequences, but the team also found non-coding RNAs representing antisense transcripts of coding sequences.

"The overall conclusion, that HCMV transcription is complex and multi-faceted, has implications for the potential sophistication of virus functionality during infection," senior author Andrew Davison, a researcher with the Medical Research Council-University of Glasgow Centre for Virus Research, and co-authors wrote. "The study also illustrates the key contribution that deep sequencing can make to the genomics of nuclear DNA viruses."

A Massachusetts-led team did a genome-wide association study using copy number data generated by comparative genomic hybridization to look for structural variations linked to height. As they report in the American Journal of Human Genetics, the investigators saw an over-representation of rare deletions in the genomes of the shortest children when they analyzed CNV information on more than 4,400 children — a pattern that they verified using data on thousands more individuals. Three regions of the genome popped out as having potential ties to height, though no clear gene candidates were found in the regions.

"Our findings strongly support the hypothesis that increasing burden of lower frequency deletions can lead to shorter stature," Children's Hospital Boston and Broad Institute researcher Andrew Dauber, co-first author of the study, said in a statement, "and suggest that this phenomenon extends to the general population."

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

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