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This Week in Nucleic Acids Research: May 2, 2013

Japanese researchers report on efforts to characterize gene expression, metabolism, growth patterns, and more in a fission yeast strain with a whittled down, or reduced representation, genome. In an effort to define a core set of essential genes, the team used a large-scale gene deletion strategy to lop off four large stretches of sequence from the already compact Schizosaccharomyces pombe genome. The resulting strain, which was missing hundreds of thousands of bases and an estimated 223 protein-coding genes, was somewhat hindered in taking up glucose and amino acids, they report. It also showed shifts in some metabolic, gene expression, and protein patterns.

Washington University's Robi Mitra and colleagues outline a method for charting DNA methylation marks in heterogeneous cells from normal or diseased tissue samples. The team demonstrated the effectiveness of this approach — called laser capture microdissection-reduced representation bisulfite sequencing, or LCM-RRBS — using tissue from mice with a type of tumor called gonadectomy-induced adrenocrotical neoplasia. The approach proved useful for comparing methylation profiles in the tumor and nearby normal tissue, study authors note, arguing that the method "will facilitate the investigation of DNA methylation in cancer and organ development."

Finally, a team from Belgium, the UK, and the US explore approaches for detecting structural variants that crop up in a single cell over the course of a cell cycle. Using paired-end sequence data from DNA from individual breast cancer or blastomere cells that had undergone whole-genome amplification, the researchers showed off their analytical methods, which make it possible to pick up copy number changes or rearrangements affecting a few dozen to thousands of DNA bases. Their analyses also looked at the artifacts introduced during whole-genome amplification process with an eye to weeding them out during structural variant detection.