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This Week in PLoS: Mar 22, 2010

Researchers report the genome sequence of Cupriavidus necator JMP134, a β-proteobacterium and pollutant degrader, in PLoS ONE this week. Its genome consists of two chromosomes and two plasmids containing 6,631 protein-coding genes. C. necator JMP134 shows the potential for catabolosim of "almost all" proteinogenic amino acids, the researchers note. "This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment," the team writes. The authors suggest that the complete genome sequence for this proteobacterium provides the basis for further study of the mechanisms and regulation of chroloaromatic compound biodegradation.

In PLoS Biology this week, researchers at the University of Zurich use a reaction-diffusion model to reveal that the reaction mechanism can "support both graded monostable and switch-like bistable gene expression, depending on whether recruited repressor proteins generate a single silencing gradient or two interacting gradients that flank a gene." The authors say their work confirms that chromosomal recruitment of activator and repressor proteins causes the stability of gene expression to be determined by the spatial distribution of silencing nucleation sites along the chromosome — a finding they suggest will help further investigations to understand the mechanisms of variegated gene expression.

Also in PLoS Biology this week, researchers at Uppsala University describe the sexually antagonistic genes of Drosophila melanogaster. In combining data on sex-specific fitness and genome-wide transcript abundance in a quantitative genetic landscape in both laboratory and wild populations, the team identified candidate genes — comprising about eight percent of the Drosophila genome — which appear to experience sexually antagonistic selection in adults. "As predicted, the X chromosome is enriched for these genes, but surprisingly they represent only a small proportion of the total number of sex-biased transcripts, indicating that the latter is a poor predictor of sexual antagonism," the authors write.

In PLoS Genetics this week, researchers in Germany and Singapore report that parental genome dosage imbalance deregulates imprinting in Arabidopsis thaliana. The team investigated the effects of DNA methylation and histone methylation in four genes in the model plant and found that genome dosage imbalance deregulated the expression of FIS2 and PHE1 in an antagonistic manner. "The complexity of the network of regulations between expressed and silenced alleles of imprinted genes activated in response to parental dosage imbalance does not support simple models derived from the parental conflict hypothesis," the researchers say.

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.