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This Week in Genome Research: Sep 16, 2015

A University of California, Berkeley- and Connecticut Health Center-led team characterizes alternative splicing events that are regulated by dozens of new and known Drosophila genes. The researchers relied on a combination of RNA interference screening and RNA sequencing to track down these splicing regulators, systematically dialing down levels of 56 suspected regulatory genes and then tracking the post-transcriptional consequences. Their results suggest that the first exon in spliced genes was most often affected when splicing regulator levels were altered. And many of the splicing events appeared to be mediated by more than one regulatory protein. Together, the study's authors say, the analysis "substantially enhances our understanding of recent models of splicing regulation and provides a resources of thousands of exons that are regulated by 56 diverse [RNA binding proteins]."

University of California, Los Angeles and UC San Diego researchers explore interactions between host genetics and the environment and their impact on gut microbial community composition in mice. With the help of 16S ribosomal RNA gene sequencing, the team tracked gut microbial community composition in mice from the Hybrid Mouse Diversity Panel — a collection comprised of more than 100 inbred mouse strains. By folding in information on genetic polymorphisms present in each strain, the investigators were able to start teasing apart heritable and environmental contributors to these microbiomes before testing the dietary response consequences of transplanting gut microbes from one strain to another.

Finally, an international group led by investigators at Uppsala University considers drivers of differentiation in sister species of flycatchers from the Ficedula genus. From patterns in 200 re-sequenced flycatcher genomes representing four Ficedula species and 10 different populations, the researchers saw signs of differentiation islands cropping up in comparable genome regions in birds from different flycatcher lineages. But rather than stemming primarily from gene flow, this differentiation appears to be due to a combination of linked selection and variable recombination rates, they note.