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This Week in Genome Research: Sep 18, 2014

A team from Spain, Ireland, and the US explored the potential fitness effects of ancient gene duplications in evolving yeast populations grown over thousands of generations. Through genome sequencing of 28 Saccharomyces cerevisiae nabbed from experimentally evolved lines produced over some 2,200 generations in the lab, the researchers found that the mutations were more apt to arise in duplicated gene pairs — particularly those generated through small-scale duplications — than in singleton genes. Similarly, glitches tended to turn up in the promoter regions of duplicates rather than singleton genes, consistent with a role for duplicated genes in both genetic and regulatory robustness.

Structural variants can prompt gains and losses in breast cancer cells that contribute to the transcriptional activity of apparent oncogenes, according to a Genome Research study by investigators based in Singapore, the US, Canada, and Mexico. The team used mate-pair sequencing on long-insert DNA, coupled with array- or sequencing-based transcriptome profiles, on eight breast cancer cell lines to retrace amplicon dynamics and their oncogenic effects. Results of the analysis pointed to interrelationships between sequential amplicon-related structural variations that appeared to prompt recurrent amplification changes in the genome, the authors report, hinting that "the genomic configuration off breast cancer may identify conjointly expressed targets for combination therapy."

Stanford University's Michael Snyder and colleagues from the US and China used an approach called chromatin interaction analysis by paired-end tag sequencing, or ChIA-PET, to explore regulatory element interactions in human cell lines. By comparing the locations of half a dozen regulatory factors with patterns detected with chromatin immunoprecipitation and RNA sequencing data, the researchers saw signs that gene expression enhancers and promoters interact differently depending on the human cell type considered. Their regulatory interaction map also revealed differences in proximal and distal chromatin states and related transcription factor binding events that seem to reflect the function and cell type specificity of the gene involved.