In Genome Biology this week, a team of researchers led by investigators at the Baylor College of Medicine in Houston, Texas, report that anatomical similarities in divergent species are "accompanied by extensive transcriptome conservation." Using RNA sequencing, the team compared the abundance and developmental regulation of all transcripts in the amoebae Dictyostelium discoideum and Dictyostelium purpureum, which "have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish." They found that, in both species, developmental regulation of transcription is highly conserved between orthologs. "These findings suggest that developmental programs are remarkably conserved at the transcriptome level, considering the great evolutionary distance between the genomes," the authors conclude.
Researchers at Uppsala University in Sweden present their novel method for de novo prediction of splice junctions in RNA-seq data in Genome Biology this week. Their technique consists of a combination of a split read alignment and their software program, SplitSeek. "When tested on mouse RNA-seq data, over 31,000 splice events were predicted, of which 88 percent bridged between two regions separated by at most 100 kb, and 74 percent connected two exons of the same RefSeq gene," the authors write, adding that their strategy also reports genomic rearrangements.
Also in Genome Biology this week, researchers in Germany report that their genome-wide mapping of the transcription factor TFIIB and antagonist negative cofactor NC2 binding sites reveals insights into the construction of the preinitiation complex. Using a ChIP-chip approach, the team interrogated TFIIB in two biological replicates from human B cell line LCL721, and concludes that "Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated."
A team of researchers employed comparative genomics in a study published this week that reveals 104 candidiate structured, non-coding RNAs from bacteria, archaea, and their metagenomes. The team identified twelve candidate metabolite-binding RNAs — three of which they validated — and novel cis-regulatory RNAs "implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection by Helicobacter, and many other physiological processes." Several of the non-coding RNA candidates were found in the metagenome DNA sequences, the researchers say, suggesting that their work lay the foundation for further investigations to validate the functions of these molecules.