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Nature Describes a Circular Consensus Sequencing Method, CRISPR Platform, More

A circular consensus sequencing method developed at Pacific Biosciences is used to de novo sequence and assemble a human genome in a study appearing this week in Nature Biotechnology. With the approach, the study's authors achieved precision and recall above 99.91 percent for single-nucleotide variants, 95.98 percent for indels, and 95.99 percent for structural variants. In addition, the researchers were able to phase nearly all variants into haplotypes. The de novo assembly produced a contig N50 above 15 megabases and was 99.998 percent concordant with the Genome in a Bottle benchmark. GenomeWeb has more on this, here

A new CRISPR platform that uses the Cpf1 endonuclease, rather than Cas9, enables inducible gene editing and gene activation in human cells, according to a report in this week's Nature Chemical Biology. The study's authors identified a pair of split Cpf1 fragments that allow for chemical- and light-inducible genome editing using chemical-inducible dimerization domains and light-inducible dimerization domains, respectively. The study's authors also identified a spontaneously activated split Cpf1 pair whose newly generated amino and carboxyl termini can be repurposed as de novo fusion sites of artificial effector domains. "Based on this finding, we generated an improved split dCpf1 activator, which has the potential to activate endogenous genes more efficiently than a previously established dCas9 activator," they write.  

A new multiplexed genome-engineering method is reported in Nature Methods this week. The approach involves encoding Cas12 and a CRISPR array on a single transcript through the addition of a stabilizer tertiary RNA structure. With this system, its developers demonstrate constitutive, conditional, inducible, orthogonal, and multiplexed genome engineering of endogenous targets using up to 25 individual CRISPR RNAs delivered on a single plasmid. 

The extinction of the cave bear, a Late Pleistocene megafauna species, may have been influenced by expanding human populations at the end of the last ice age, according to a large-scale mitogenomic analysis published this week in Scientific Reports. The study's authors combined hybridization capture and next-generation sequencing to reconstruct 59 new complete cave bear mitochondrial genomes from 14 sites in Western, Central, and Eastern Europe. They then compared these genomes to 64 published cave bear mtDNA sequences to reconstruct the population dynamics and phylogeography during the Late Pleistocene. The scientists find five major mitochondrial DNA lineages, pointing to a "noticeably more complex biogeography of the European lineages during the last 50,000 years than previously assumed." Further analysis suggests that the cave bear population was stable until a drastic decline starting around 40,000 years ago, coinciding with the spread of anatomically modern humans in Europe.