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This Week in PNAS: Jun 12, 2018

In the early, online version of the Proceedings of the National Academy of Sciences, researchers from the University of Colorado, Boulder, the University of British Columbia, and Temple University explore alternative splicing patterns in common domesticated sunflowers and their wild ancestor Helianthus annuus. The team used a combination of seedling transcriptome sequencing and available genomic data to find more than 200 alternatively spliced transcripts, along with related quantitative trait loci in the wild and domesticated sunflower plants. Despite the rapid splicing shifts found in the domestic plants, particularly in seed-development-related genes, the authors note that "relatively few regulatory switches affecting many proteins have been altered in domesticated sunflowers."

A Memorial Sloan Kettering Cancer Center-led search for factors contributing to EGFR inhibitor acquired resistance in lung adenocarcinoma. With the help of transposon mutagenesis screening, the researchers systematically introduced more than 1,900 transposon insertions in an EGFR-mutant cell line, looking for alterations associated with resistance to the EGFR tyrosine kinase inhibitor (TKI) afatinib. Along with clinical sequencing data for 136 individuals with EGFR-mutant lung adenocarcinomas that became resistant to EGFR inhibition, the screen led to resistance-related insertions affecting the MET gene, as well as YES1 amplifications. They saw similar amplifications in a subset of TKI-resistant lung cancers containing ALK fusions. 

Iowa State University researchers consider gene-environment interactions in relation to flowering time with a long-term study of two inbred sorghum populations grown under seven environmental field conditions. The team narrowed in on nearly 9,000 sorghum SNPs with genotyping-by-sequencing, using information at almost 1,500 variants to put together genetic maps to help tease out flowering time determinants in various environments for the model crop plant, among other analyses. "[W]e first uncovered the pattern of genotype response to different environments," the authors say, and "then uncovered the pattern generated by the combination of environmental factors and the pattern of genetic effects at the individual gene level across environments."