In Nature this week, researchers from the Lawrence Berkeley National Laboratory report data showing that the fruit fly transcriptome is far more complex than previously thought. They examined various Drosophila cultured cell lines at different developmental stages and dissected organ systems, revealing new genes, proteins, and transcripts, including hundreds of previously unidentified long non-coding RNAs. Notably, transcripts and expression patterns were found to be similar to those in other animals, suggesting that some mechanisms are conserved in metazoans.
Meanwhile, in Nature Biotechnology, a team from the University of California, Berkeley, publish details of an automated process for genome annotation that integrates RNA-seq and gene-boundary datasets. Dubbed Generalized RNA Integration Tool, or GRIT, the approach was applied to Drosophila short-read RNA-seq, cap analysis of gene expression, and poly(A)-site-seq data collected for the modENCODE Project, allowing the researchers to recover the vast majority of previously annotated transcripts while doubling the total number of transcripts cataloged. Overall, GRIT showed 30 percent higher precision and recall than popular transcript assembly tools.