In Genome Biology this week, a trio of researchers describes their computational approach to identify miRNAs from high-throughput sequencing data, miRTRAP. When applied to the chordate Ciona intestinalis, the team distinguished nearly 400 reported miRNA loci; previously, 80 had been identified and reported. Almost half of the genes identified produce non-conventional miRNA products, the authors write, including moRNAs and antisense miRNAs.
In another Genome Biology methods paper, Masako Suzuki and colleagues at the Albert Einstein College of Medicine in New York report their optimized procedures for the analysis of tag-based cytosine methylation assays. Using EcoP15I, a type III restriction-modification enzyme, Suzuki et al. "isolated sequences flanking sites digested by the methylation-sensitive HpaII enzyme or its methylation-insensitive MspI isoschizomer for massively-parallel sequencing." Their method, the authors write, allows users to more accurately quantify methylation at more than 1.8 million loci in the human genome.
Harvard Medical School and Dana-Farber Cancer Institute researchers report their genome-wide functional analysis of 5' untranslated region introns in humans this week. Because "introns in 5'UTRs differ from those in coding regions and 3'UTRs with respect to nucleotide composition, length distribution and density," the team investigated 5'UTR introns on the genome scale. They found that "genes with regulatory roles were surprisingly enriched" in having 5'UTR introns of human non-receptor protein tyrosine kinases. "Our results suggest that human 5'UTR introns enhance the expression of some genes in a length-dependent manner," the team suggests, adding that their findings convey that complex evolutionary forces act on this group of introns.
Researchers report their phylogenetic analyses of gene duplications in early eukaryotes. "Among nearly 2600 orthogroups identified, at least 300 of them still retain duplication that occurred before the divergence of the three kingdoms," the authors write, adding that their investigation shows that many gene duplications occurred early on in eukaryotic evolution. The team suggests that perhaps these duplications were the effect of "one or more large-scale duplications, possibly whole genome or segmental duplication(s), which provides a genomic basis for the successful radiation of early eukaryotes."