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This Week in PNAS: Apr 28, 2015

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from India report on epigenetic alterations in the blood that coincide with the development of high-altitude pulmonary edema, or HAPE. The team used a genome-wide association study and targeted sequencing to search for HAPE-related variants in more than 200 individuals — a group that included affected individuals, unaffected visitors to high altitude locations, and healthy native individuals acclimated to the high altitude sites. The search led to risk variants in and around genes from the so-called apelin system. But the study's authors also identified shifts in methylation in individuals with HAPE, including methylation changes coinciding with lower-than usual expression of the apelin gene.

An Ohio State University Comprehensive Cancer Center-led team took a closer look at a low-penetrance chromosome 9 SNP linked to papillary thyroid cancer risk in past genome-wide association studies. By fine-mapping the region with targeted sequencing, the researchers narrowed in on a linkage disequilibrium block spanning more than 30,000 bases that coincided with enhanced thyroid cancer risk. The thyroid cancer-associated block included a handful of enhancer elements that appear to contribute to long-range regulation of genes such as FOXE1 and PTCSC2.

Researchers from Taiwan used array-based transcriptome profiling of maize leaves collected at different stages of leaf development. Based on the gene expression patterns detected in nine new transcriptomes and 13 transcriptomes established for developing maize leaves during a previous study, the team identified genes with elevated or diminished leaf expression during the first week or so after maize seeds were planted. The study's authors also came up with a scheme for predicting transcription factor binding sites at play during this time, uncovering 1,340 new predicted transcription factor binding sites and more than 250 new interactions that appear to occur between transcription factors and these binding sites.