In Nature this week, Jay Shendure and his colleagues at the University of Washington in Seattle report their 3D model of the Saccharomyces cerevisiae genome. In capturing both intra- and inter-chromosomal interactions, the team was able to compose a map, at kilobase resolution, of the haploid yeast genome. "Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur," the authors write, adding that their "findings provide a glimpse of the interface between the form and function of a eukaryotic genome."
In an advance, online publication of Nature Biotechnology this week, researchers in Korea and the UK describe their "analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccgaromyces pombe." When compared with gene dispensability in budding yeast, the team found that 83 percent of "single-copy orthologs in the two yeasts had conserved dispensability," though dispensability differed for particular pathways in each. The authors also suggest that "fission yeast has more essential genes than budding yeast," and that nonessential genes are likely to be present in a single copy.
An international research team reports in Nature this week that cell signaling by microRNAs 165/6 directs gene dose-dependent root cell fate in plants. Short Root and Scarecrow, both transcription factors, activate miR165a and miR166b, which then act to degrade their combined target: "mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery," the authors write, adding that "the resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner."
In Nature Genetics, researchers report that de novo copy number variations in the Shank2 synaptic folding gene link autism-spectrum disorder and intellectual disability. "DNA sequencing of SHANK2 in 396 individuals with ASD, 184 individuals with mental retardation and 659 unaffected individuals (controls) revealed additional variants that were specific to ASD and mental retardation cases, including a de novo nonsense mutation and seven rare inherited changes," the authors write.