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This Week in PNAS: Oct 16, 2013

Francis Collins and colleagues from the National Human Genome Research Institute, the Lawrence Berkeley National Laboratory, the University of California, San Francisco, and the US Department of Energy's Joint Genome Institute report on a role for so-called stretch enhancers in cell type-specific gene expression. The team performed a series of high-throughput transcriptome- and chromatin immunoprecipitation-sequencing experiments on human pancreatic islet cells, before folding in data on nine more cell types assessed through ENCODE. Together, the study's authors say, findings from these and other experiments indicate that the long enhancer sequences are "critical chromatin elements for coordinating cell type-specific regulatory programs." Variants linked to common diseases in genome-wide association studies are particularly common in stretch enhancers too, they note, hinting that the regions could influence the risk of such conditions.

In another study appearing in the early, online edition of the Proceedings of the National Academy of Sciences this week, a team from the University of Utah, Boston University, and Brigham Young University describes a computational method for estimating gene activity with barcodes gleaned from data generated with a range of different gene expression profiling platforms and approaches. The researchers demonstrated the applicability of this "Universal exPression Code," or UPC, algorithm using microarray and RNA sequencing data for liver and kidney samples, for instance, showing that the approach can estimate whether genes of interest are on or off in each individual sample.

A group from the US and Germany looks at ways in which signaling stemming from the epidermal growth factor receptor, or EGFR, influences the activity of fruit fly enhancer elements acting on a transcription factor called Broad. With the help of a computational model that considers network interactions and dynamics, the investigators determined that two enhancers acting in concert to control Broad transcription factor expression during the process of Drosophila oogenesis are themselves under the control of an EGFR signaling gradient.