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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.

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.