In a paper published online in advance in Genome Biology, the Weizmann Institute of Science's Sivan Navon and Yitzhak Pilpel suggest that codon distribution along genes affects translation efficiency, which they deduced based on synthetic expression libraries in Escherichia coli. Overall, Navon and Pilpel say that their "study demonstrates how synthetic biology complements bioinformatics by providing a setup for well-controlled experiments in biology."
Harvard's Shirley Liu and her colleagues present MM-ChIP, a method to abate cross-platform and between-laboratory variation as a result of ChIP-chip or ChIP-seq data integration. MM-ChiP, Liu et al. write, "improves both the sensitivity and the specificity of detecting ChIP-enriched regions, and is a useful meta-analysis tool for driving discoveries from multiple data sources."
Investigators at the University of Chicago and the University of Oxford characterized methylation at more than 22,000 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals and found "180 CpG-sites in 173 genes that were associated with nearby SNPs," they report in a Genome Biology paper published online in advance. Using RNA-seq, the Chicago-Oxford team identified expected "negative correlations between promoter methylation and gene expression levels … across genes." The researchers also report significant SNP overlapping, "associated with both methylation and gene expression levels."
A team led by researchers at Italy's Sapienza Università di Roma describes the "coding potential of the products of alternative splicing in human" in a recent Genome Biology paper. After using mass spec to identify alternative splicing isoforms, the team analyzed their functional domains and investigated "the plausibility of their predicted [structures]." The team concludes that while its "strategy for correctly identifying translated products consists on relying on the conservation of active sites," when combined with modeled isoform structure plausibility experiments, it "increases both coverage and specificity with a moderate cost in terms of sensitivity."