In Genome Research this week, an international research team reports the use of mRNA-seq and agnostic splice site discovery methods to "advance mRNA-seq bioinformatics toward unbiased transcriptome capture," the potential importance of which they've shown in an in vivo model of neurological disease. In applying the method to the L4 dorsal root ganglion of rats with chronic neuropathic pain, the team found that "12.4 percent of known genes were induced and seven percent were repressed in the dysfunctional" L4 DRG. They also identified 10,464 novel exons, 21.9 percent of which were dysregulated. "mRNA-seq with agnostic analysis methods appears to provide a highly productive approach for in vivo transcriptomics in the nervous system," the authors conclude.
Researchers at the University of Zurich, Switzerland, present their meta-analysis of microbial lineages using environmental and whole-genome sequence data in Genome Research this week. By grouping publicly available ribosomal RNA sequences "into operational taxonomic units at various levels of resolution, and systematically" searching for "co-occurrence across environments," the team found that "naturally occurring microbes indeed exhibited numerous, significant inter-lineage associations."
A pair of investigators from the University of Otago, New Zealand, show that co-option and gene duplication in the Drosophila Enhancer of Split Complex — parts of which are modulators of Notch signaling — has played a role in the evolution of genomic regulation. "The complex is well conserved in insects but is highly modified in Drosophila, where two of the ancestral genes of the complex are missing, and the remaining two have been duplicated multiple times," the authors write, adding their hypothesis that the E(spl)-C complex is regulated by Notch in a genomic domain that has been conserved in Arthropods for nearly 520 million years.
In a Genome Research perspectives piece, James Noonan at the Yale University School of Medicine discusses recent "efforts to obtain genomic sequence from Neanderthal." A critical implication of the Neanderthal genome sequence, Noonan suggests, will be the examination of the evolutionary relationship between humans and Neanderthals. When it comes to these analyses, the author writes, "there is a long road ahead, and we should not be surprised if we discover that we are not as different from our extinct relatives as we believe."