The University of Washington's Jay Shendure and colleagues present a strategy for mapping enhancers and their gene targets across the genome with a combination of CRISPR/Cas9-based editing and single-cell RNA sequencing. The team's "expression quantitative trait locus (eQTL)-inspired framework" upends potential gene regulators in individual cells with random CRISPR interference events before profiling the single cell transcriptomes. When they used this approach to interrupt more than 5,900 candidate enhancers in the human genome, for example, the authors identified 664 apparent cis enhancer-gene pairs with the help of nearly 255,000 single-cell transcriptomes.
A Florida State University-led team explores regulatory elements that control DNA replication timing and compartmentalization in mammalian cell nuclei. By interfering with topologically associating domains (TAD) in mouse embryonic stem cells with CRISPR-based gene editing, the researchers profiled the cis-regulatory elements involved in early versus late DNA replication, chromatin architecture, compartmentalization, and more. "Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide [replication timing], A/B compartmentalization, TAD architecture, and transcription," the authors write, "revealing fundamental principles linking genome structure and function."
Researchers from the University of California, San Francisco, and elsewhere share results from a comparative protein interaction analysis of dengue and Zika viruses. Using affinity purification-mass spectrometry, RNA interference, reporter assays, network analyses, and other approaches, the team searched for protein-protein interactions specific to ZIKVs or DENVs in human hosts or to DENVs in mosquito hosts, along with protein-protein interactions shared between the flaviviruses. Based on conserved interactions between human and flavivirus proteins, for example, the authors saw that a viral protein called NS5 appears to quell the activity of genes stimulated by interferon signaling, while their ZIKV-specific analysis led to protein interactions that provided potential clues to microcephaly.