Gerstein et al., Comparative analysis of the transcriptome across distant species, Nature, in press, 2014.
The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discovered co-expression modules shared across animals, many of which are enriched in developmental genes. We used expression patterns to align the stages in worm and fly development, finding a novel pairing between worm embryo and fly pupae, in addition to the expected embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we found that the extent of non-canonical, non-coding transcription is similar in each organism, per base-pair. Finally, we found in all three organisms the gene-expression levels, both coding and noncoding, can be quantitatively predicted from chromatin features at the promoter using a “universal model," based on a single set of organism-independent parameters.
16 human, worm and fly co-expressed and co-evolved modules showing highly coordinated expression patterns only during phylotypic stage, tarball of csv files: 16_module.tar.gz
