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This Week in Genome Biology: May 20, 2009

In an article in last week's Genome Biology, scientists used sys bio tools to study how some highly disordered proteins avoid degradation in order to carry out their function. Combining sequencing, gene expression, and proteomic information, they were able to see that not only do disordered proteins have a greater proportion of predicted ubiquitination sites, but also their transcripts have higher proportions of predicted miRNA target sites and higher mRNA decay rates. Even though this suggests that disordered proteins and their transcripts "are present in the cell at low levels and/or for a short time before being targeted for disposal," the researchers also found that for a "significant proportion" of them, estimates for miRNA targets, ubiquitination, and mRNA decay rate are low, possibly a mechanism for leaving some to do their job in the cell.

Also from last week, Sanger researchers compared the genome sequences of three strains of the soil bacteria, Pseudomonas fluorescens, strains SBW25, Pf0-1, and Pf-5. They found that the genomes are very diverse, sharing only 61 percent of their genes. Using a functional genomic in vivo expression technology (IVET) screen of SBW25, they identified 125 plant-induced genes with many functions specific to the plant environment.

In a paper appearing this week, researchers led by Frank Uhlmann of Cancer Research UK, the UK's leading cancer charity, performed a high-resolution analysis of cohesin localization along chromosomes of fission yeast. Even though recent genome-wide surveys show a difference in localization in different organisms, their results suggest that "features that were thought to differentiate cohesin between organisms collectively define the overall behavior of fission yeast cohesin," they write. Among others, they found that in fission yeast, cohesin was detected at chromosomal loading sites in regions of strong transcriptional activity.

In work published online today, University of Leeds scientists used whole genome sequencing of a recombinant Toxoplasma gondii strain to study recombination between different strains, finding that "recombination between clonal lineages does occur in nature but there is nevertheless close homology between African and North American isolates." They used 454 sequencing of a type II/III recombinant isolate, TgCkUg2, and compared this to seven other isolates from Uganda. TgCkUg2 was shown to contain entire chromosomes of either type II or type III origin demonstrating chromosome sorting rather than intrachromosomal recombination, they say.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.