In the April issue of Genome Research, Harvard's Martha Bulyk and Josh LaBaer led research that scanned yeast transcription factors for their binding specificity across the genome. Building off ChIP-chip data, they created genome-wide binding profiles for 89 known and predicted yeast TFs over more than 2.3 million gapped and ungapped 8-bp sequences, finding 50 new or different DNA-binding site motifs. In total, they write, "this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities."
Other work published in early online looks at the molecular relationship between a mammalian transcription factor and its DNA binding motif. Taking the transcriptional repressor REST (NRSF) as their study focus, they show that canonical motifs that lead to strong binding control REST targets that are common to all cell types, while weak binding between the two control targets that are cell- or tissue-specific. Most surprisingly, they say, weak binding sites are part of DNA sequences with the highest levels of evolutionary constraint.
Several groups have integrated bioinformatics data to study functional networks. In one paper, published early online, Stockholm Bioinformatics Center scientists have developed a method to predict interactome networks. FunCoup supports interactions ranging from physical interaction, protein complex member, metabolic, or signaling link. Testing their model on more than 50 data sets in seven organisms, FunCoup predicted global networks in eight eukaryotes, they say. In other work, researchers at Merck's Rosetta Inpharmatics integrated siRNA screening and protein-protein interaction data to find a novel candidate gene for type 2 diabetes, S1pr2.
Finally, scientists led by those at DOE have sequenced the complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B. Not only did they find evidence of thermophilic adaptiveness, but they also identified new secreted glycoside hydrolases and carbohydrate esterases in the genome, "revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism." Many of these enzymes, they say, break down plant cells walls, fungal cell walls, or storage carbohydrates glycogen and trehalose.