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This Week in Cell: Feb 6, 2019

Researchers from the UK, Sweden, and Finland explore T helper immune cells features with the help of gene editing in primary mouse cells, documenting factors that regulate the differentiation of T helper type 2 (Th2) cells involved in mammalian adaptive immunity. The team relied on almost a dozen CRISPR-Cas9 genetic screens, RNA sequencing, sequencing-based methods for mapping chromatin accessibility, and mouse-human comparisons to uncover overlapping Th2 cell activation and differentiation factors. "We demonstrate that these two processes are tightly coupled," the authors explain, "and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs."

A University of Washington-led team tallies structural variants in long-read sequenced human genomes. Among the 99,604 sequence-resolved insertions, deletions, and inversions — found in 11 newly sequenced genomes from individuals in African, Asian, European, American, and South Asian populations or in four hydatidiform mole or Asian individual genomes sequenced in prior studies — the team saw more than 2,200 structural variants shared across the discovery genomes. The authors took that structural variant set forward for further testing in another 440 genomes, demonstrating that structural variants, and particularly variable number of tandem repeats, are enriched toward the ends of chromosomes.

Finally, investigators in Italy, Spain, the US, and the UK present almost 155,000 microbial genomes, identified in 9,428 metagenomes representing individuals from 32 countries who were sampled at up to four body sites. The collection of 154,723 microbial genomes spanned new and known bacteria and archaea, including unknown and uncultured species found in the oral microbiomes of individuals with Westernized or non-Westernized lifestyles, the authors report. "The resulting genome set can … serve as the basis for future strain-specific comparative genomics to associate variants in the human microbiome with environmental exposures and health outcomes across the globe," they write. GenomeWeb has more on the study, here.