Bacterial adaptive immune systems employ CRISPRs (clustered regularly interspaced short palindromic repeats) and CRISPR-associated (Cas) proteins for RNA-guided nucleic acid cleavage1,2. Although generally targeted to DNA substrates3–5, the Type III and Type VI CRISPR systems direct interference complexes against single-stranded RNA (ssRNA) substrates6–9. In Type VI systems, the single-subunit C2c2 protein functions as an RNA-guided RNA endonuclease9,10. How this enzyme acquires mature CRISPR RNAs (crRNAs) essential for immune surveillance and its mechanism of crRNA-mediated RNA cleavage remain unclear. Here we show that C2c2 possesses a unique ribonuclease activity responsible for CRISPR RNA maturation that is distinct from its RNA-activated ssRNA-degradation activity. These dual ribonuclease functions are chemically and mechanistically different from each other and from the crRNA-processing behavior of the evolutionarily unrelated CRISPR enzyme Cpf111. We show that the two ribonuclease activities of C2c2 enable multiplexed processing and loading of guide RNAs that in turn allow for sensitive cellular transcript detection.

The RNA-guided CRISPR-associated protein Cas9 is used for genome editing, transcriptional modulation, and live-cell imaging. Cas9-guide RNA complexes recognize and cleave double-stranded DNA sequences on the basis of 20-nucleotide RNA-DNA complementarity, but the mechanism of target searching in mammalian cells is unknown. Here, we use single-particle tracking to visualize diffusion and chromatin binding of Cas9 in living cells. We show that three-dimensional diffusion dominates Cas9 searching in vivo, and off-target binding events are, on average, short-lived (<1 second). Searching is dependent on the local chromatin environment, with less sampling and slower movement within heterochromatin. These results reveal how the bacterial Cas9 protein interrogates mammalian genomes and navigates eukaryotic chromatin structure.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human host cells via angiotensin-converting enzyme 2 (ACE2) and causes coronavirus disease 2019 (COVID-19). Here, through a genome-wide association study, we identify a variant (rs190509934, minor allele frequency 0.2–2%) that downregulates ACE2 expression by 37% (P = 2.7 × 10−8) and reduces the risk of SARS-CoV-2 infection by 40% (odds ratio = 0.60, P = 4.5 × 10−13), providing human genetic evidence that ACE2 expression levels influence COVID-19 risk. We also replicate the associations of six previously reported risk variants, of which four were further associated with worse outcomes in individuals infected with the virus (in/near LZTFL1, MHC, DPP9 and IFNAR2). Lastly, we show that common variants define a risk score that is strongly associated with severe disease among cases and modestly improves the prediction of disease severity relative to demographic and clinical factors alone.

Human infection with SARS-CoV-2, the causative agent of COVID-19, leads to a remarkably diverse spectrum of outcomes, ranging from asymptomatic to fatal. Recent reports suggest that both clinical and genetic risk factors may contribute to COVID-19 susceptibility and severity. To investigate genetic risk factors, we collected over 500,000 COVID-19 survey responses between April and May 2020 with accompanying genetic data from the AncestryDNA database. We conducted sex-stratified and meta-analyzed genome-wide association studies (GWAS) for COVID-19 susceptibility (positive nasopharyngeal swab test, ncases=2,407) and severity (hospitalization, ncases=250). The severity GWAS replicated associations with severe COVID-19 near ABO and SLC6A20 (P<0.05). Furthermore, we identified three novel loci with P<5x10-8. The strongest association was near IVNS1ABP, a gene involved in influenza virus replication, and was associated only in males. The other two novel loci harbor genes with established roles in viral replication or immunity: SRRM1 and the immunoglobulin lambda locus. We thus present new evidence that host genetic variation likely contributes to COVID-19 outcomes and demonstrate the value of large-scale, self-reported data as a mechanism to rapidly address a health crisis.

We report the results of a comprehensive investigation of the recently discovered stereoselective and controlled polymerization of racemic lactide (D,L-LA) using an initiator prepared in situ from indium(III) chloride (InCl(3)), benzyl alcohol (BnOH), and triethylamine (NEt(3)). Linear relationships between number-average molecular weight (M(n)) and both monomer to alcohol concentration ratio and monomer conversion are consistent with a well-controlled polymerization. Studies on polymerization kinetics show the process to be first-order in [InCl(3)](0) and zero-order in both [BnOH](0) and [NEt(3)](0). The rate of D,L-LA conversion is also dependent on the indium(III) halide (i.e., t(1/2)(InCl(3)) approximately = 43 min versus t(1/2)(InBr(3)) approximately = 7.5 h, 21 degrees C, CD(2)Cl(2), [D,L-LA](0)/[BnOH](0) approximately = 100, [D,L-LA](0) = 0.84 M, [InX(3)](0)/[BnOH](0) = 1) and lactide stereoisomer (i.e., k(obs)(D,L-LA) approximately = k(obs)(meso-LA) > k(obs)(L-LA)). A model system that polymerizes D,L-LA with the same high degree of stereoselectivity was developed using 3-diethylamino-1-propanol (deapH) in lieu of BnOH and NEt(3). The product of the reaction of deapH with InCl(3) was identified as [InCl(3)(deapH)(H(2)O)](2) by elemental analysis, X-ray crystallography, and NMR and FTIR spectroscopies. An anhydrous version of the complex was also isolated when care was taken to avoid adventitious water, and was shown by pulsed gradient spin-echo (PGSE) NMR experiments to adopt a dinuclear structure in CD(2)Cl(2) solution under conditions identical to those used in its stereoselective polymerization of D,L-LA. The combined data suggest that the initiating species for the InCl(3)/BnOH/NEt(3) system is similar to [InCl(3)(deapH)(H(2)O)](2) and of the type [InCl((3-n))(OBn)(n)](m). With this information we propose a mechanism that rationalizes the observed stereocontrol in D,L-LA polymerizations. Finally, in an exploration of the scope of the InCl(3)/BnOH/NEt(3) system, we found this system to be effective for the polymerization of other cyclic esters, including epsilon-caprolactone and several substituted derivatives.

Data availabilitySummary statistics generated by COVID-19 Host Genetics Initiative are available online (https://www.covid19hg.org/results/r6/). The analyses described here use the freeze 6 data. The COVID-19 Host Genetics Initiative continues to regularly release new data freezes. Summary statistics for samples from individuals of non-European ancestry are not currently available owing to the small individual sample sizes of these groups, but the results for 23 loci lead variants are reported in Supplementary Table 3. Individual-level data can be requested directly from the authors of the contributing studies, listed in Supplementary Table 1.

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The discovery of the CRISPR-Cas9 endonuclease has enabled facile genome editing in living cells and organisms. Catalytically inactive Cas9 (dCas9) retains the ability to bind DNA in an RNA-guided fashion, and has additionally been explored as a tool for transcriptional modulation, epigenetic editing, and genome imaging. This Review highlights recent progress and challenges in the development of dCas9 for imaging genomic loci. The emergence and maturation of this technology offers the potential to answer mechanistic questions about chromosome dynamics and three-dimensional genome organization in vivo.