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This Week in Nature: Oct 12, 2017

In this week's Nature is a series of studies that collectively provide a comprehensive atlas of variation in gene expression across diverse tissues of the human body and among individuals. The studies are based on data from the Genotype Tissue Expression (GTEx) consortium, which collected and analyzed more than 7,000 post-mortem samples from 449 otherwise healthy human donors across 44 tissues. In one study, consortium scientists used expression quantitative trait loci mapping to find that local genetic variation affects gene expression levels for the majority of human genes. They also identify inter-chromosomal genetic effects for 93 genes and 112 loci, and "demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease." In a second study, researchers used GTEx data to examine impact of rare variation on gene expression. By combining data across multiple tissues, they curated a set of gene expression outliers that replicated at higher rates and showed stronger enrichment of rare variants than those from any single tissue. They also found that rare structural variants, frameshift indels, coding variants, and variants near the transcription start site were most likely to have large effects on expression. In two other studies, investigators used GTEx data to look at how genetic variants associated with gene expression can regulate RNA editing and X-chromosome inactivation, respectively. GenomeWeb has more on these studies, here.

And in Nature Genetics, a group led by scientists from the National Cancer Center Singapore and Duke-NUS Medical School in Singapore report the full genome sequence of the durian fruit, which is known for its unique flavor and pungent smell. The team assembled a high-quality reference genome from a Musang King durian fruit stalk using complementary single-molecule DNA sequencing and chromosome scaffolding techniques. Comparative analyses with other related plants reveal an ancient whole-genome duplication event in durian that is likely shared with cotton. Further analysis showed higher levels of activity for sulfur metabolism genes during ripening in fruit organs compared with non-fruit organs. GenomeWeb also covers this, here.