By searching through eukaryotic genome sequences for proteins with conservation or divergence patterns similar to those of known small RNA proteins, Harvard University's Gary Ruvkun and his colleagues were able to uncover new small RNA pathway proteins involved in silencing, as they report in an article published online in Nature this week. They applied a non-binary phylogenetic profiling method to cluster 20,000 Caenorhabditis elegans proteins as encoded by the genomes of some 85 other species, including animals, plants, and fungi. From this, they developed a list of proteins that have phylogenetic profiles similar to those of Argonaute RDE-1, MUT-2, and RNA-dependent RNA polymerases. Additionally, the researchers used a Bayesian method to integrate their phylogenetic analyses with findings from other studies, including functional genomic screens or proteomic studies of small RNA pathways. "Many of the newly identified small RNA pathway proteins are orthologues of proteins implicated in RNA splicing," the researchers write. "In support of a deep connection between the mechanism of RNA splicing and small-RNA-mediated gene silencing, the presence of the Argonaute proteins and other small RNA components in the many species analysed strongly correlates with the number of introns in those species."
Over in Nature Biotechnology this week, researchers led by the Chinese Academy of Sciences' Wen Wang from the Chinese Academy of Sciences present their de novo genome sequence of the domestic goat, Capra hircus. The researchers used Illumina sequencing to develop a sequence assembly that they then fleshed out by using OpGen's Argus system and its GenomeBuilder hybrid assembly software to develop even longer scaffolds — closer to the size of chromosomes. From their annotation and transcriptomic work, the researchers note that the goat appears to have an expansion in the ferritin heavy chain gene family and that cashmere-producing goats show 51 genes, many of which were keratin genes, with at least two-fold changes in expression between different hair follicle types.
Our sister publication GenomeWeb Daily News has more on this study here.
Bianca Heemskerk, Pia Kvistborg, and Ton Schumacher write in The EMBO Journal that advances in cancer genomics are allowing researchers and physicians to get a glimpse of patients' tumor-specific antigens that comprise their "cancer antigenome." The trio writes that "the clinical use of such epitopes to induce or enhance tumour-specific T-cell reactivity should be considered as a form of personalized medicine ('personalized cancer immunotherapy')."