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This Week in Genome Research: Nov 8, 2017

Researchers from Tufts and Duke universities describe a whole-genome nanopore long-read sequencing strategy for profiling complex genomic rearrangements formed by faulty DNA double-strand break repair. The team applied the approach to finding GAA trinucleotide microsatellites and following the processes forming them in several strains of the yeast model organism Saccharomyces cerevisiae. "Our results demonstrate that nanopore sequencing is an effective and efficient method of identifying novel [complex genomic rearrangements] in S. cerevisiae, which provided important insights into the mechanisms of DNA repair." 

A team from Germany, Switzerland, the US, and Sweden considers sex-biased microRNA expression features that might contribute to sexual dimorphism in mammals and birds. Using small RNA sequencing, the researchers assessed miRNA patterns in dozens of male and female mouse, gray short-tailed opossum, and red jungle fowl tissues. The most pronounced sex-biased differences in miRNA expression turned up in liver and heart tissue from male and female mice, they report, though the analysis highlighted several other examples. For their follow-up experiments, the authors explored regulatory features behind such sex-biased miRNA levels. 

Finally, Australian researchers introduce an analytical method for teasing out genomic rearrangements from massively parallel sequencing data. The positional de Bruijn graph assembly-based approach — known as the "Genome Rearrangement Identification Software Suite," or GRIDSS — is designed to identify genomic rearrangements based on assembly, split read, and read pair data, the team explains. The investigators note that they applied GRIDSS to simulated, cell line, and tumor sequence data, uncovering a range of structural variants called at low or high confidence with a favorable false-discovery rate.