Researchers at the University of Massachusetts Medical School report on the combined experimental and bioinformatic approach they used "to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus, and Schizosaccharomyces japonicus" in a paper published online in advance in Genome Biology this week. The team mapped nucleosome occupancy by deep sequencing mononucleosomal DNA from the species, "finding that origins tend to occupy nucleosome-depleted regions," it writes.
In another paper published online in advance this week, a team led by investigators at the National Institute of Diabetes and Digestive and Kidney Diseases examines autosomal dosage compensation in Drosophila , reporting on its investigation of 21 DrosDel deficiency lines from chromosome arm 2L — a test set the researchers say "allowed us to look at one-dose genes in five regions with multiple deficiencies [to] explore the question of whether compensation is a property of individual genes or particular deficiencies." Overall, the team found that gene-specific dose responses vary. "Expression of two-dose genes that are first-degree neighbors of one-dose genes in novel network models also changed expression, and the directionality of change depended on the response of one-dose genes," the authors write.
Elsewhere in the journal, the Wellcome Trust Sanger Institute's David Adams and his colleagues present a computational approach to identify RNA editing sites by taking an initial set of transcriptome-genome mismatch sites and filtering those calls, accounting for systematic biases in alignment, single nucleotide variant calling, and sequencing depth.