Published in last week's Genome Biology, Steve Jacobsen and team performed a genome-wide study to characterize the patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana. Using chIP-chip, they found, among other things, that all three types of H3K4me are "almost exclusively genic" while two-thirds of Arabidopsis genes have at least one type of H3K4me. Also, H3K4me2 and H3K4me3 are found mostly in promoters and 5' genic regions, while H3K4me1 is found within transcribed regions.
This week, scientists from the Institut Pasteur in Paris published work that investigated the source of ORFans (ORFs without matches in current sequence databases) in archaeal and bacterial genomes. Their large-scale survey of potentially recently acquired integrative elements – viruses, plasmids, and transposable elements versus genes acquired by horizontal gene transfer – in 119 archaeal and bacterial genomes showed that 56 percent of new clusters of atypical genes are likely IE, whereas only 7 percent likely originated via HGT, they say. Moreover, their study "contributes to the issue of the origin of ORFans, because 39% of these are found inside [Clusters of Atypical Genes], many of which likely represent recently acquired IE."
Jo Vandesompele is senior author on a paper also appearing this week on a new method to normalize miRNA RT-qPCR data. In this study, his team used a mean expression value of all expressed microRNAs in a sample as a normalization factor for miRNA real-time quantitative PCR data and compared it to what's currently used, showing that the mean expression value "outperforms the current normalization strategy in terms of better reduction of technical variation and more accurate appreciation of biological changes," they say in the abstract.
A group of European scientists led by Simon Dittami of the Station Biologique in France have done the first large-scale transcriptomic study of a brown alga, Ectocarpus siliculosus. Under short-term abiotic stress of three types, they saw that unlike terrestrial plants, E. siliculosus "undergoes extensive reprogramming of its transcriptome," including expression changes of almost 70 percent of its genes.
Finally, researchers at the University of Toronto have performed a comparative analysis of metabolism across 193 eukaryotes. Using whole and partial genome and proteome datasets, they found that metabolic enzymes are, in general, "highly conserved," but that certain pathways are more highly conserved than others and that there is a "highly conserved, but nonetheless flexible, 'core' of enzymes largely involved in multiple reactions across different pathways."