In a paper published online in advance in Nucleic Acids Research this week, researchers at the University of Vienna and elsewhere present a Web server for the prediction of small RNA targets, RNApredator. The team says RNApredator users can select from more than 2,155 genomes and plasmids from 1,183 bacterial species to interrogate putative sRNA targets. Unlike other servers that perform similar tasks, the Vienna-led team says that "RNApredator takes the accessibility of the target during the target search into account, improving the specificity of the predictions," adding that, while similar to that of more complex approaches, its underlying programming "needs at least three orders of magnitude less time to complete."
In another Nucleic Acids Research advance online publication, Columbia University's Markus Fischer et al. present a Web server for the analysis and comparison of proteins' structural and functional properties, which they've named MarkUs. "In contrast to a ‘structure in/function out’ approach to protein function annotation, the server is designed to be highly interactive and to allow flexibility in the examination of possible functions, suggested either automatically by various similarity measures or specified by a user directly," Fischer and his colleagues write.
A team led by investigators at the Cincinnati Children's Hospital Medical Center describes in a paper recently published online in advance in Nucleic Acids Research the human DEK oncogene's roles in DNA damage response signaling and double-strand break repair. In human cancer cell lines and xenografts, the team found DEK depletion "sufficient to induce a DNA damage response as assessed by detection of γH2AX and FANCD2."
The University of Melbourne's Matthew Young et al. report their use of ChIP-seq to assemble genome-wide maps of H3K27me3 enrichment, with which they "identified three enrichment profiles with distinct regulatory consequences" in a recent Nucleic Acids Research paper. Among the three, the researchers say they were surprised to find an enrichment profile "with a peak in the promoter of genes that is associated with active transcription." In each of the three, the researchers found genes present "in different proportions in … the cell types studied." Overall, Young et al. say that its ChIP-seq analysis "will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation."