In the early, online edition of the Proceedings of the National Academy of Sciences, a team from the Czech Republic and Germany describes horizontal gene transfer in plants from different grass families. With targeted PCR screening on 16 barley plants, the researchers found evidence of nuclear ribosomal RNA genes that appeared to originate in plants from a lineage that split from the barley plant family roughly 60 million years ago. "The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral," they say.
Researchers from Denmark, Switzerland, and Spain explore selection patterns in great apes through comparative genomics for another PNAS paper. Using SNP profiles in genome sequences for dozens of gorillas, chimpanzees, orangutans, bonobos, and humans, the team considered genetic diversity across the genome, uncovering a dip in diversity near genes that was more pronounced in great apes with larger population sizes. "We infer that the impact of selection on the genomic diversity of a species increases with the effective population size," the authors write, "most likely due to the differential influx rate of beneficial mutations."
An American and Swiss team takes a look at interactions between transcription factors, enhancers, and gene expression in mouse adipocyte cells. With the help of massively parallel reporter assays and binding assays, the researchers considered more than 32,000 natural or synthetic enhancers, looking at factors that impact binding and enhancer activity at the PPAR-gamma transcription factor. Their results indicate that both sequence motifs and broader genomic features such as chromatin accessibility impact PPAR-gamma binding, for example, while enhancer activity appears to be influenced by combinatorial transcription factor interactions.