In an advance online publication of Genome Research this week, researchers at various institutions in China report their functional annotation of the Oryza sativa indica and japonica rice transcriptomes at single-nucleotide resolution using RNA-seq. The team identified more than 15,000 novel transcriptional active regions "of which 51.7 percent have no homolog to public protein data and [more than] 63 percent are putative single-exon transcripts, which are highly different from protein-coding genes." Their subsequent comparative transcriptome analysis revealed that 3,464 genes showed differential expression patterns between the rice models.
A team led by Yu Qiu at the University of California, San Diego, this week demonstrates the "structural and operational complexity of the Geobacter sulfurreducens genome." By integrating "proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 5′-end transcripts," the team writes, they obtained "a most precise annotation." Structural, operation, and functional annotations, when combined, yield a "three-level annotation that greatly expands our understanding of prokaryotic genomes," Qiu et al. suggest.
A public-private research collaboration led by investigators at Rosetta Inpharmatics this week reports their "systematic genetic and genomic analysis of cytochrome P450 activities in the human liver." Most P450s, the team found, "were positively correlated among themselves and were highly correlated with known regulators as well are thousands of other genes enriched for pathways relevant to the metabolism of drugs, fatty acids, amino acids, and steroids." In their subsequent genome-wide association analyses of genetic polymorphisms and P450 expression showed that certain sets of SNPs are associated with P450 traits, and, further, "suggested the existence of both cis-regulation of P450 expression (especially for CYP2D6) and more complex trans-regulation of P450 activity," the authors write.
And in a Genome Research methods paper published online in advance, investigators at the Richmond, Calif.-based Sangamo BioSciences and their industrial and academic colleagues describe their approach for "functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome." ZFNs, the authors write, allow for targeted transgenesis "at a frequency of up to 15 percent following transient transfection of both transformed and primary human cells." Upon addition to this locus, transgenes "exhibit consistent expression and sustained function over 50 cell generations," the authors write.