The Genome Institute at Washington University's Li Ding and colleagues outline a bioinformatics tool for integrating information from various fusion and breakpoint prediction algorithms to find gene fusions and discern the rearrangements that formed them. The team demonstrated the effectiveness of this method, known as BreakTrans, first using whole-genome and whole-transcriptome sequence data from a breast cancer. From there they applied BreakTrans to data from 43 breast cancer samples assessed through the Cancer Genome Atlas — an analysis that unearthed 90 gene fusions matching verified rearrangements in the genome.
Austrian and German researchers used nucleic acid probes to explore the nature and extent of non-sequence-specific interactions between proteins and nucleic acids in human cells for another Genome Biology study. The team nabbed proteins out of whole-cell extracts from three human cell lines with the help of affinity purification and 25 rationally designed RNA and DNA probes. The nearly 750 proteins isolated in such experiments were identified by mass spectrometry and assessed for their nucleic acid binding preferences. "The dataset described here represents a rich resource of experimentally determined nucleic-acid binding proteins," study authors say, "and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms."
Using a combination of computational modeling, in vivo assays, and chromatin immunoprecipitation sequencing, researchers from France, the US, and Belgium traced interactions between the Drosophila transcription factor Shavenbaby and the genes it targets in so-called trichome cells during fruit fly embryogenesis. Results of their analysis revealed a wide swath of terminal effector genes that Shavenbaby regulates during the late stages of fruit fly embryogenesis, along with some of the features found in these enhancers.