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This Week in Genome Research: Apr 8, 2009

In early online edition this week, Canadian scientists used whole genome sequencing on three strains of Streptococcus pneumoniae that had been made resistant to the antibiotic linezolid. Comparative analysis revealed mutations in the 23S rRNA gene in all mutants and at G2576T, a previously recognized resistance mutation. Mutations in an additional 31 genes were also found in at least one of the three genomes. Gene inactivation experiments showed mutations upstream of the ABC transporter genes spr1021 and spr1887 to be correlated with increased expression of these genes and neighboring genes of the same operon, they say in the abstract.

In this month's issue, there's a review on using paired-end tag sequencing for a variety of genomic analyses. Paired-end tag protocols have been developed for everything from transcriptome analysis to analyzing transcription factor binding sites, epigenetic sites such as histone modification sites, and genome structures. The advantage, the authors say, is the ability to uncover linkages between the two ends of DNA fragments. "Using this unique feature, unconventional fusion transcripts, genome structural variations, and even molecular interactions between distant genomic elements can be unraveled by PET analysis," they write in the abstract.

Alu elements, which make up 11 percent of the genome, use retrotransposition to insert genes into the genome that cause disease. In this study, scientists at the Tulane University Health Sciences Center analyzed the difference between the older and younger subfamilies to see why only the ones belonging to the younger families are active. After analyzing the sequence differences of the Alu elements, they found that the "length of the longest number of uninterrupted adenines in the A-tail, the degree of A-tail heterogeneity, the length of the 3' unique end after the A-tail and before the RNA polymerase III terminator, and random mutations found in the right monomer all modulate the retrotransposition efficiency."

Mark Stoneking at the Max Planck Institute for Evolutionary Anthropology in Leipzig led work that looked at the human salivary microbiome. Analysis of 14,115 partial 16S ribosomal RNA sequences from saliva samples from 120 healthy individuals revealed much diversity. The rRNA belonged to 101 known bacterial genera, and phylogenetic analysis suggested that an additional 64 unknown genera are present, they say. "Further characterization of the enormous diversity revealed here in the human salivary microbiome will aid in elucidating the role it plays in human health and disease."

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.