In a paper published online in advance in Genome Biology this week, a trio of researchers at Harvard University presents "a high-resolution map of a cyanobacterial transcriptome" — that of Synechococcus elongatus PCC 7942. Using RNA-seq, tiling expression microarrays, and RNA polymerase ChIP-seq, the team identified "several interesting features at promoters, within transcripts and in terminators relating to transcription initiation, elongation, and termination," it writes, adding that it also uncovered "many putative non-coding transcripts."
In another Genome Biology advance online publication, Nancy Cox and her colleagues at the University of Chicago present a genome-wide method to identify copy number variants "that contribute to heterogeneity in drug response," with a focus on drugs "widely used in anticancer treatment regimens." By examining copy number variants identified through population-scale array-based and sequencing-based surveys, the team found that "although SNPs tag some of the CNVs associated with drug sensitivity, several of the most significant CNV-drug associations are independent of SNPs; consequently, they represent genetic variations that have not been previously interrogated by SNP studies of pharmacologic phenotypes," it writes.
An international team led by investigators in Australia this week shows that filamentous Ascomycete fungi appear to have evolved in a novel way in which "genes are conserved within homologous chromosomes, but with randomized orders and orientations." More specifically, the researchers say that "this mode of evolution is designated mesosynteny," but that the mesosynteny they observed "appears to be restricted to filamentous Ascomycetes and was most striking between species in the Dothideomycetes." Such mesosynteny in Ascomycete fungi, they continue, "could be explained by a high frequency of chromosomal inversions, but translocations must be extremely rare. The mechanism for this phenomenon is not known, but presumably involves generation of frequent inversions during meiosis."
The University of California, Berkeley's Christopher Miller et al. this week present EMIRGE, "a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances." EMIRGE allows researchers to recover ribosomal small subunit genes by assembling short read sequence data, and thus allows them to refine taxonomic characterizations of microbial communities, Miller and his colleagues write in Genome Biology.