In work out of Ian Holmes' UC Berkeley lab, a team describes as new genome browser, JBrowse, published in this week's early online edition of Genome Research. The browser is open source, portable, and JavaScript-based, and differs from other available browsers in that it uses less server power. "JBrowse helps preserve the user's sense of location by avoiding discontinuous transitions, instead offering smoothly-animated panning, zooming, navigation and track selection," says the abstract.
Also in advanced publication, a paper from Greg Hannon's lab with first author Emily Hodges had used array capture coupled with bisulfite sequencing to map genome-wide DNA methylation in a mammalian genome. Looking across 324 randomly selected CpG islands representing more than 25,000 CpG sites, they found 25 percent of the islands showed complex methylation patterns.
Scientists at the Nijmegen Centre for Molecular Life Sciences in the Netherlands looked at epigenetic changes associated with X inactivation in mice ES cells. Using chIP-chip, chIP-seq, and expression analysis, they saw that only in female ES cells is there an increase in H3K27me3 deposition across the X chromosome as inactivation happens during differentiation. "This indicates deposition of H3K27me3 during XCI being tightly associated with the act of silencing of individual genes across the [inactive X chromosome]," they write.
In this month's issue, work led in part by the University of Michigan's Inhan Lee and Subramanian Ajay has found a new class of miRNA targets that have both 5'-UTR and 3'-UTR interaction sites. Using model systems, they show that there are "combinatory interactions" between an miRNA and both end regions of an mRNA and call this new class of targets, miBridge. This makes for "an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3'-UTR alone."