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Researchers the world over are fast adopting CRISPR-Cas9 to tinker with the genomes of humans, viruses, bacteria, animals and plants. Nature brings together research, reporting and expert opinion to keep you abreast of the frontiers of gene editing.
Genome editing could be applied to correct disease-causing mutations in human embryos, but concerns about efficacy and safety are paramount. Shoukhrat Mitalipov and colleagues use CRISPR–Cas9 to correct a heritable cardiomyopathy mutation in human embryos. By optimizing the experimental conditions, the authors show very reduced mosaicism, and report that for this heterozygous mutation, CRISPR–Cas9-induced breaks seem to be preferentially repaired using the wild-type allele as a template in human embryos. The results advance our understanding of the promises and challenges of editing the human germline.
CRISPR–Cas systems provide defence against invasive genetic elements in prokaryotes. They function by detecting and degrading invader transcripts, mainly through RNA-guided recognition and interference. Csm6 is a CRISPR-associated ribonuclease known to degrade invasive transcripts, but how its activity is regulated by invader sensing was unknown. Here, the authors find that Csm6 is activated by a cyclic oligoadenylated second messenger generated by Cas10 activity within the type III interference complex. This novel mechanism of CRISPR interference regulation, which resembles an aspect of mammalian innate immunity, expands the toolkit of prokaryotic immunity strategies.
It is difficult to establish cell division history and lineage relationships for tissues that are not easily accessed. DNA barcoding approaches can provide this information, but do not offer spatial data. This collaboration between the labs of Long Cai and Michael Elowitz harnesses the power of CRISPR/Cas9-mediated mutagenesis and multiplexed single-molecule RNA fluorescence hybridization (smFISH) to build a new tool, termed MEMOIR, which they use to follow mouse embryonic stem cell divisions. MEMOIR gives access to lineage information in situ and at the single-cell level, while at the same time monitoring changes in gene expression state.
The CRISPR–Cas9 nucleases now widely used in gene editing can be readily customized, but can also induce substantial genome-wide off-target mutations at sequences that resemble the on-target site. Keith Joung and colleagues report a high-fidelity variant of Cas9 from Streptococcus pyogenes that shows on-target activities comparable to the wild-type enzyme, but with off-target events that are undetectable by genome-wide break capture and targeted sequencing methods.
The protozoan parasite Cryptosporidium is a major cause of diarrhoeal disease in young children but until now it has been difficult to study and there is currently no vaccine and only a single drug (nitazoxanide) available to counter the infection. Here Boris Striepen and colleagues describe a robust genetic system for cryptosporidiosis. They genetically modify Cryptosporidium parvum by optimizing transfection of sporozoites using a CRISPR/Cas9 system, to generate stable transgenic lines suitable for in vitro and in vivo drug screening. Using this system they knockout the gene encoding thymidine kinase which increases susceptibility to trimethoprim, an antimalarial drug to which wild-type Cryptosporidium is resistant.
The once fanciful idea that bacteria might have immunological memory became accepted fact with the discovery that the CRISPR–Cas gene loci evolve rapidly to acquire short phage sequences, or spacers, which then integrate between CRISPR repeats and constitute a record of phage infection. These spacers are transcribed into small CRISPR RNAs (crRNAs) that are used to target the DNA of invading viruses. Two papers published in this issue of Nature describe molecular details about how bacteria create a DNA memory of the invading virus. Jennifer Doudna and colleagues show that the purified Escherichia coli Cas1–Cas2 complex integrates oligonucleotide DNA substrates into acceptor DNA in a manner similar to retroviral integrases and DNA transposases. Cas1 is the catalytic subunit, while Cas2 increases integration activity; together they form the minimal machinery required for spacer acquisition. Luciano Marraffini and colleagues show that in the type II CRISPR–Cas system of Streptococcus pyogenes, the Cas9 nuclease that inactivates invading viral DNA using the crRNA as a guide is also required for the incorporation of new spacer sequences, by a yet to be determined mechanism.
The CRISPR-Cas9 system has emerged as a powerful tool for genome editing and transcriptional regulation of specific genes. Feng Zhang and colleagues have successfully modified the system to specifically and potently activate endogenous gene transcription on a genome-wide scale, such that it can be used for large-scale functional genomics screens. Application to a genome-wide screen of melanoma cells for genes which when overexpressed can confer resistance to a BRAF inhibitor demonstrates the feasibility of such screens, and also led to the discovery of potential new resistance mechanisms.
A bacterial enzyme that uses guide RNA molecules to target DNA for cleavage has been adopted as a programmable tool to site-specifically modify genomes of cells and organisms, from bacteria and human cells to whole zebrafish.