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This Week in Genome Research: Apr 29, 2009

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.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.