Researchers from Australia's Commonwealth Scientific and Industrial Research Organization have developed a genetic "clock" that can predict the lifespans of vertebrate species, including extinct ones. Using reference genomes of 252 vertebrate species with known lifespans, the scientists identified 42 genes in which the density of cytosine-phosphate-guanosine (CpG) sites — which are targets of DNA methylation — is highly predictive of maximum lifespan in vertebrates. They use their findings to develop a model to estimate lifespan in extinct animals including the wooly mammoth and long-lived species such as the Rougheye rockfish. "Our study adds lifespan to the range of significant ecological parameters that can be provided by molecular biology," the authors write in Scientific Reports.
A new method for fast and accurate long-read assembly is presented in Nature Methods this week. The assembler — called wtdbg2 — was developed by collaborators from the Chinese Academy of Agricultural Sciences and Harvard Medical School, and is two- to 17-times as fast as published tools while achieving comparable contiguity and accuracy. "Affordable population-scale long-read sequencing is on the horizon," the scientists write. "Wtdbg2 is an assembler that is able to keep up with the throughput and the cost."
Modifications that can boost the genome-editing efficacy of CRISPR-Cas9 in clinically relevant primary cell types are reported in Nature Biotechnology this week. A group led by scientists from the University of California, San Francisco, show how truncated Cas9 target sequences added at the ends of a homology-directed repair (HDR) template interact with Cas9 ribonucleoproteins (RNPs) to transport the template to the nucleus, enhancing HDR efficiency as much as fourfold. Additionally, stabilizing the RNPs in nanoparticles improved editing efficiency by around twofold. Combining these two improvements increased gene targeting efficiency even at reduced HDR template doses, yielding approximately two-to-six times as many viable edited cells across multiple genomic loci in diverse cell types, the researchers write. The work, they add, has direct translational potential for research, biotechnology, and clinical applications.