🧬 PubMed RNA Editing Daily Digest

RNA editing enzymatically modifies RNA molecules post-transcriptionally, enabling precise sequence alterations. Advantages include reversibility and temporal control without genomic DNA changes, allowing dynamic regulation of gene expression while preserving original genetic information. In this study, we characterized McAgo derived from Monosporascus cannonballus, which functions as a programmable nuclease guided by 14-30 nt gRNAs, demonstrating robust RNA cleavage activity at physiological temperature. Furthermore, we delivered McAgo RNP (ribonucleoprotein) complexes into mammalian cells, achieving >90% RNA knockdown efficiency with minimal innate immune responses. A catalytically inactive mutant (dMcAgo) using a gRNA as short as 20 nt, conjugated to the hADAR2 deaminase domain (hADAR2dd E488Q), achieved up to 90% RNA editing efficiency in vitro. This study establishes, for the first time, the effective targeting of endogenous RNA by a heterologous Argonaute in mammalian cells, alongside its demonstrated utility for RNA editing-thereby expanding the functional repertoire of Argonaute proteins.

Rewriting RNA information to alter function requires controllable tools to edit RNA sequences within a user-defined region. Here we report a single-strand deaminase-assisted platform for adjustable RNA information manipulation (AIM). AIM is composed of a loop-forming guide RNA bound to an RNA-targeting Cas protein and an evolved TadA. AIM induces a loop, flanked by paired regions, in the target RNA; the loop size can be adjusted to allow conversions of single and multiple bases. We evolve TadA to achieve A-to-I, C-to-U or simultaneous A+C editing in coding and noncoding regions. We apply AIM to suppress the ochre nonsense codon (UAA) in disease-relevant cell and animal models, in which the two As must be simultaneously edited to rewrite the coding information. Moreover, we use AIM to manipulate adjacent phosphorylation sites important for protein function. Collectively, AIM is a versatile platform for manipulating RNA information within user-defined regions, opening additional avenues for functional RNA modulation.

The CRISPR-Cas13 system exhibits potent RNA cleavage activity and has been widely utilized for RNA-targeting applications. However, its collateral cleavage of bystander RNAs limits

The recent discovery of the type III-E class of CRISPR-Cas effectors has reshaped our fundamental understanding of CRISPR-Cas evolution and classification. Type III-E effectors are composed of several Cas7-like domains and a single Cas11-like domain naturally fused together to create a single polypeptide capable of targeting and degrading RNA. Here we identified a novel type III-E-like effector composed of three Cas7 domains and a Cas1 domain which was not active but could be engineered into an active chimeric RNA-targeting Cas effector by domain additions and swaps from other type III-E effectors. The results reveal that various domains in type III-E effectors can be swapped for the equivalent domain from a different type III-E effector. Remarkably, the Cas1 domain located at the C-terminus of Cas7-1 could be swapped in place of the Cas11 domain located between the Cas7.1 and the Cas7.2 domains of DiCas7-11. The results reveal a new modality for engineering type III-E effectors from the blueprints found in nature.

Alpha-1 antitrypsin deficiency (AATD) is both a gain- and loss-of-function disease that impacts the liver and lung. Most severe cases result from a homozygous missense mutation in the SERPINA1 gene (Z mutation). While current therapies and those in development may ameliorate lung or liver disease, few are designed to address both. We have developed SERPINA1-994, an N-Acetylgalactosamine-conjugated chemically modified oligonucleotide that elicits adenine-to-inosine RNA editing using endogenous adenosine deaminases acting on RNA enzymes, to correct SERPINA1 Z transcripts. We show that SERPINA1-994 edits 50% of the Z transcript in hepatocytes of NSG-PiZ mice, which increases total serum AAT levels and induces the production of wild-type M-AAT protein. SERPINA1-994 addresses loss of AAT function in lung by increasing the neutrophil elastase inhibition capacity of mouse serum and gain of function in liver by correcting gene expression patterns, decreasing Z-AAT protein aggregation and decreasing inflammation. SERPINA1-994 relies on a clinically proven delivery technology and directs highly specific RNA rather than DNA editing with no bystander editing. Overall, these data suggest that SERPINA1-994 changes a ZZ homozygous state, which is associated with a high risk for AATD, to a low-risk MZ-like phenotype.