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This Week in PNAS: Jul 23, 2013

In a study slated to appear in the early, online version of the Proceedings of the National Academy of Sciences this week, the University of Washington's Evan Eichler and colleagues report on retrotransposon rates and profiles present in the genomes of great apes. Using sequence data from 10 humans and 83 apes that were sequenced for the Great Ape Diversity Project, the team identified tens of thousands of fixed and polymorphic mobile element insertions in the great ape genomes. These represented insertions associated with L1 elements and with Alu retrotransposons, researchers noted, which appeared to be more variable and prone to increases and decreases in recent great ape evolutionary history.

The genes expressed in specific parts of the chicken brain do not necessarily correspond with those activated in developmentally homologous regions of the mouse brain, according to another PNAS study. Researchers from the UK, the US, and Chile used comparative transcriptomics and gene co-expression analyses to look at more than 5,000 genes expressed most prominently in different parts of the chicken and mouse brains. Their findings suggest that "adult gene expression does not cleanly and consistently fit any model based exclusively on developmental cell lineage or cellular characteristics … regions that have common developmental origins, but show functional divergence, exhibited no greater transcriptomic similarity than developmentally unrelated but functionally comparable regions."

Finally, a group based in Israel, Germany, and the US relied on chromatin immunoprecipitation coupled with tiling arrays, together with other types of analyses, to chart nucleosome occupancy patterns across the human cytomegalovirus genome during different stages of infection. Data generated for cytomegaloviruses grown in human cell lines offered hints about nucleosome dynamics in the viral genome — along with a peek at the DNA sequence and non-sequence-based protein factors associated with this process during early and late stages of infection, respectively.