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This Week in Nucleic Acids Research: Mar 14, 2018

Researchers from the US and China introduce a computational pipeline known as SEASTAR ("systematic evaluation of alternative transcription start sites in RNA") for uncovering examples of alternative first exon use in transcriptomes from different organisms, cell types, and/or biological conditions, based on RNA sequence data. After demonstrating that transcription start sites and first exons found with SEASTAR lined up well with results from CAGE experiments, the team applied the approach to mouse fibroblast cells undergoing reprogramming to produce induced pluripotent stem cells. The authors note that such experiments not only uncovered "dynamic temporal changes in the usage of alternative first exons," but also transcription factor expression shifts.

A University of North Carolina-led team considers potential ties between copy number changes, DNA methylation profiles, and gene expression patterns across human tumors from half a dozen cancer types profiled for the Cancer Genome Atlas. With the help of a computational method meant to address cell type composition-related confounders, the researchers looked at copy number, methylation, and expression associations in breast cancer, colon cancer, prostate cancer, glioblastoma, leukemia, and lower-grade glioma. "Our results suggest that jointly studying multiple types of omic data to infer both tumor purity and cell type composition is a promising approach," they conclude.

Washington State University researchers explore several variants in the telomere replication complex component gene CTC1, in an effort to tease out the pathogenic mutations behind a genetic condition called Coats plus syndrome that affects a wide range of body systems. The team used chromosome breakage, immunoprecipitation, and other assays to track the genome stability and interaction consequences of 11 CTC1 missense mutations or small deletions that were previously implicated in Coats plus syndrome. "Our results show that these mutations induce spontaneous chromosome breakage and severe chromosome fragmentation that are further elevated by replication stress," the authors report, "leading to global genome instabilities."