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This Week in Genome Research: Mar 5, 2014

A University of Southern California- and Nara Medical University, Japan-led team took an array-based look at the DNA methylation changes that occur in human intestinal cells in the wake of surgical tissue transplantation. By comparing methylation levels in intestinal epithelial cells before and after surgery to reconstruct a bladder from intestinal tissue, the researchers demonstrate that the intestinal cells in the newly formed "neobladder" take on distinct epigenetic features over time, moving away from their original tissue-specific methylation profiles. "The dynamic resetting of [the] DNA methylome in the neobladder not only implicates local environmental cues in the shaping and maintenance of the epigenome," researchers write, "but also illustrates an unexpected cross-talk between the epigenome and cellular environment."

The University of Michigan's Patricia Wittkopp and colleagues did a series of RNA sequencing experiments in Drosophila from various species, strains, and hybrid fruit flies to get a sense of the regulatory networks controlling gene expression in the flies. Their results suggest regulatory features influencing gene expression are more prone to change and divergence than gene expression itself — a situation that seems to stem from changes that compensate for some regulatory shifts. The analysis also uncovered differences in nature and rate of gene expression regulation that were specific to certain Drosophila lineages.

Transposable elements are frequently traded between plants through horizontal gene transfer, according to another Genome Research study. Researchers from France and the US sorted through existing sequence data from 40 representatives from a range of plant families, searching for examples of horizontal transfer involving LTR-retrotransposons. In 26 of those genomes, they saw evidence of one or more transposable elements originating from horizontal transfer. The events weren't restricted to closely related species and occurred between distantly related species, the study authors note, though they appear somewhat more common within related plant groups.