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This Week in Nucleic Acids Research: Jun 8, 2016

Researchers from the University of Bergen and Harvard University outline updates to the web tool CHOPCHOP, which is designed to guide CRISPR- and TALEN-based genome engineering efforts. Version two of the database is decked out with new tools to support updated CRISPR approaches, including those that involve Cpf1 and Cas9 nickase enzymes, the team notes, while allowing for custom length single-guide RNAs. The update is also intended to boost the efficiency and targeting of the site through an updated user interface. The study's authors say the site currently includes genome editing support for nearly three dozen organisms and accepts request for new annotated sequences.

A team from Sweden and Korea takes a computational look at the metabolic signaling networks present in hepatocellular carcinoma. Reasoning that fatty liver disease is a risk factor for the liver cancer, the researchers first characterized lipid pathways based on available signaling and interactome data, using these networks to interpret RNA sequencing data for HCC patients profiled in the Cancer Genome Atlas database and other large repositories. "[W]e identified significant dysregulated expressions of lipid-regulated genes, across many different lipid metabolic pathways," the authors say, noting that "viral hepatitis causes HCC by a distinct mechanism, less likely involving lipid anomalies."

Italian researchers report on the human retina transcriptional atlas they developed by doing RNA sequencing on 50 retina samples from deceased, visually impaired donors. Their experiments uncovered more than 77,600 gene transcripts with new and known isoforms, while quantifying expression patterns for known transcripts. The team notes, for example, that some 65 percent of Gencode genes are expressed in the retina, though expression variability exists between individuals.