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This Week in Genome Biology: Jun 13, 2018

Researchers from the Barcelona Institute of Science and Technology and elsewhere present findings from a negative selection analysis of cancer genomes. With the help of exome sequence data for more than 7,500 tumors from 26 cancer types, the team searched for regions of the tumor genome that are relatively impervious to mutation. Such negative selection turned up in nearly two dozen tumor genes, the authors note, including essential cancer genes, translation and transport genes, and parts of the genome coding for "immune-exposed proteins." "Our simulation indicates that the increasing availability of sequencing data from individual tumor types will help us to reveal tissue-specific or even patient-specific traces of negative selection," they write, noting that this may "improve our understanding of cancer-essential functions in different tissues and enable us to develop strategies capable of targeting cancer type-specific essential genes or activating the immune system through optimized modification of epitopes."

A Kyoto University- and RIKEN-led team introduce a microfluidics-based system for characterizing nuclear and cytoplasmic RNAs from a single cell. The approach, known as SINC-seq, involves separating RNA in the nucleus from that in the cytoplasm, before establishing distinct nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) libraries, the researchers explain. With this strategy, they not only quantified nucRNA and cytRNA, but also got a glimpse at the RNA content within the full cell. The authors applied the approach to human leukemic and erythroid cells under a range of conditions, revealing a shift in the relative representation of nucRNAs and cytRNAs in cells treated with a histone deacetylase inhibitor.

Researchers from Nanjing Agricultural University's Center of Pear Engineering Technology Research and other centers in China, the US, and New Zealand compare Asian and European pear domestication using re-sequencing data for 113 cultivated and wild pear accessions. Using insights from more than 18.3 million SNPs found in the pears — including 63 Asian accessions and 50 accessions from Europe — the team untangled phylogenetic relationships between the plant populations as well as their population structure and evolutionary histories. In particular, the results point to a split between Asian and European pears, followed by pear diversification, spread, and mixing. "Population structure analysis provided new evidence to support the admixed genetic background of some pear species," the authors add, "which was likely driven by self-incompatibility."