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This Week in Cell: Jun 19, 2013

Researchers from Emory University, the University of Massachusetts, and elsewhere consider contributors to the genome's three-dimensional structure during cellular differentiation in Cell. Using immunofluorescence microscopy, quantitative real-time PCR, sequencing, and other approaches, the team tracked genome structure and chromatin interactions at seven main genomic loci in mouse stem cells and differentiating neural progenitor cells, while at once looking at sets of architectural proteins participating in genome organization. "Our analyses reveal that distinct combinations of architectural proteins shape the [three-dimensional] organization of mammalian genomes at different length scales for unique functional purposes during lineage commitment," study authors say.

Some of the cellular machinery that spurs messenger RNA degradation in the cytoplasm can also signal back to the nucleus to prompt new gene expression, according to another Cell study. The Technion-Israel Institute of Technology's Mordechai Choder and colleagues from other international centers did genomic run-on experiments and other studies of yeast missing specific components of the so-called mRNA decaysome. Their results suggest mRNA decay factors shuttle back and forth between the cell's cytoplasm and the nucleus — not only prompting cytosplasmic mRNA degradation but also kick-starting gene expression in the nucleus, when needed, via interactions with transcription start sites.

A National Institutes of Health-led team takes a look at processes that let loose the expression of key genes when lymphocyte immune cells spring into action. The researchers focused on single-stranded DNA, mapping these molecules across the genome in mouse immune cells. Together with total RNA, messenger RNA, and promoter profiling information before and after immune cell activation, the single-stranded RNA patterns helped the group unravel steps involved in transcriptome activation in the lymphocytes. In particular, the work suggests that melting at already-poised promoters allows for the expression of genes amplified upon lymphocyte activation.