In PLoS One this week, researchers suggest that "re-annotation should be considered to be an essential first step for deriving value from functional genomics data" because it can produce unique knowledge derived from previous research findings. In any systems biology modeling of functional genomics data, the authors say, structural and functional re-annotation is critical — particularly for species with recently sequenced genomes. To exemplify this, the team quantified the impact of their structural and functional re-annotation of a microarray that was developed as a tool for disease research; they found that re-annotation improved both the quality and quantity of annotations and allowed for "a more comprehensive Gene Ontology-based" model.
This week in PLoS Genetics, researchers at the National Institute on Aging and their colleagues describe their investigation of the "correlation between common genetic variability across the human genome, gene expression, and DNA methylation, within human brain." They show that DNA methylation and RNA expression patterns vary across different sections of the brain, and an abundance of cis-regulated mRNA expression. The authors "show for the first time abundant quantitative trait loci for DNA CpG methylation across the genome."
Also in PLoS Genetics, an international research team reports the draft sequence of the plant-growth promoting endophytic bacterium Enterobacter sp. 638 genome. Their annotations revealed a set of genes related to the plant niche adaptation of the bacterium, including those that code for survival in the rhizosphere, root adhesion, and establishment inside the plant, among others. Their findings also point to an explanation for the bacterium's interactions with its host, the poplar tree. "This information can be further exploited to improve establishment and sustainable production of poplar ... using endophytic bacteria such as Enterobacter sp. 638 as growth promoting agents," the team concludes.
And in PLoS Biology, an international research team reports that "a large fraction of extragenic RNA Pol II transcription sites overlap enhancers" in mammalian genomes. By interrogating chromatin signatures, the team classified extrangenic Pol II binding sites and found that 70 percent of the peaks their study generated "were associated with genomic regions with a canonical chromatin signature of enhancers." Transcribed enhancers, they found, "were under purifying selection and contained binding sites for inflammatory transcription factors ... suggesting their functionality." The team suggests that their study will aid in future annotations of mammalian genomes.