In Genome Biology this week, Christian Soellner and Gavin Wright of the Sanger Institute discuss a protein interaction screen in zebrafish to identify novel ligands that bind to the ectodomains of 150 zebrafish neural receptor proteins. In screening almost 7,600 interactions, they built a network of 34 cell surface receptor-ligand pairs, while further analysis showed "surprising quantitative variation in receptor binding strengths," they say.
University of Pennsylvania scientists studied the genome-wide transcriptional activity of LINE1 elements, retrotransposons that make up almost 20 percent of the human genome and are typically not transcribed. They cloned ESTs from human lymphoblastoid cell lines of 692 L1 element sites, including 410 full-length elements, and found four of the 410 full-length elements to be differentially expressed in different members of European-American families. While many L1 element sites are expressed in human somatic tissues, they found, "few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels," says the abstract.
Led by Detlef Weigel, scientists at the Max Planck Institute for Developmental Biology in Tübingen, Germany, developed an alignment software that matches short reads against more than one reference genome. Called GenomeMapper, it "supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure."
Indiana University's Justen Andrews was lead author on work that constructed the first "genome-wide functional gene network in Drosophila melanogaster." Combining available genetic interaction, protein-protein interaction, and microarray expression data, they were able to create an integrated network covering 85 percent of the currently known genes, and their "high-confidence" network included 20,000 functional relationships among 5,021 genes.