A novel approach for combinatorial single-cell CRISPR screens is described in this week's Nature Biotechnology by University of California, San Francisco, and Princeton University researchers. The method, called direct-capture Perturb-seq, involves sequencing expressed single-guide RNAs alongside single-cell transcriptomes. This enables detection of multiple distinct sgRNA sequences from individual cells, allowing pooled single-cell CRISPR screens to be paired with combinatorial perturbation libraries that contain dual-guide expression vectors, the team writes. Using direct-capture Perturb-seq, the scientists show that targeting individual genes with multiple sgRNAs per cell improves efficacy of CRISPR interference and activation, and that hybridization-based target enrichment allows sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.
A discussion of the potential of CRISPR in food crop breeding is presented in Nature Food this week. Scientists from the University of Copenhagen and the Chinese Academy of Sciences provide an overview of the genome-editing technology and how it is currently being used for crop improvement, and offer predictions on new applications in food science. Lastly, the team discusses the regulatory landscape for gene-edited crops.
A high-quality chromosome-level reference genome for the sterlet sturgeon, Acipenser ruthenus, is reported in Nature Ecology & Evolution this week, providing insights into the evolution of this lineage of ancient and polyploid fish. The work, led by scientists from the University of Würzburg, reveals a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, as well as a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. "Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process," the researchers write. "While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random." The Scan has more on this, here.