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Genomics In The Journals: Apr 21, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A genome-wide association study in the early, online version of Nature Genetics has tracked down a trio of endometrial cancer-associated variants at a chromosome 17 locus. An international research team used Illumina arrays to genotype 1,265 Australian and British individuals with endometrial cancer and 5,190 unaffected individuals from the Wellcome Trust Case Control Consortium. They then used follow-up genotyping in nearly 11,000 individuals with or without the disease to home in on an endometrial cancer associated locus near HNF1B — a transcription factor gene linked to prostate cancer in the past.

A phylogenetic study in BMC Evolutionary Biology suggests modern day land plants share a closer evolutionary relationship with streptophyte algae than to stonewort algae. Researchers from Germany and Canada brought together information on 129 nuclear genes from dozens of plant and algae taxa. From their phylogenetic analyses, the team concluded that green land plants are more likely to have descended from ancestors of conjugating green algae in the Zygnematales order than from stonewort algae, which have reproductive patterns more closely resembling land plants.

"[D]espite their apparent simplicity, Zygnematales have genetic traces of other complex traits also associated with green land plants," corresponding author Burkhard Becker, a botanist at the University of Cologne, said in a statement. "Consequently, Zygnematales true place as the closest living relative to land plants has been revealed."

A common genetic variant in the promoter of the mucin 5B gene MUC5B can increase the risk of rare pulmonary fibrosis conditions by up to 20 times for homozygous individuals, according to a study in the New England Journal of Medicine. American and Icelandic researchers first did a genetic linkage screen to narrow in on a region of interest on chromosome 11 in individuals from 82 families affected by either idiopathic pulmonary fibrosis or familial interstitial pneumonia. Their follow-up genotyping, targeted re-sequencing, and case-control association experiments in hundreds more individuals with IPF, FIP, and unaffected controls pointed to a variant called rs35705950 that falls in a regulatory region of MUC5B and coincides with enhanced expression of the gene.

Broad Institute Genome Sequencing and Analysis Co-Director Chad Nusbaum and his team outline findings from their comparison of four fission yeast genomes in Science. By sequencing the Schizosaccharomyces octosporus, S. cryophilus, and S. japonicus genomes and weighing these against the S. pombe genome, the researchers were able to put together a Schizosaccharomyces phylogeny. Together with transcriptome data, the comparison provided insights into everything from gene expression and regulation patterns to gene, centromere, and genome structure in the fission yeast.

"Our comparative analysis of genome structure and expression in the fission yeast, especially the analysis of centromere structure and evolution, demonstrates how chromosomal features can be rearranged while retaining function and maintaining stable positions across taxa," researchers concluded. "As these results demonstrate, comparative analyses improve the power of fission yeast as a model for eukaryotic biology."

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

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