🧬 PubMed RNA Editing Daily Digest

Plants possess a unique C-to-U RNA editing mechanism mediated by PPR-DYW proteins, wherein the PPR domain recognizes specific RNA sequences while the DYW deaminase domain precisely edits the target C base-a process essential for functional protein expression in plant chloroplasts and mitochondria. The coordination of these two domains is considered crucial for precise RNA editing. In nature, this site-specific and precise base editing by PPR-DYW proteins distinguishes them from other base-editing deaminases. However, the absence of structures containing both PPR and DYW domains has limited our understanding of the precise RNA-editing mechanism of PPR-DYW proteins. Here, we present crystal structures of the consensus PPR-DYW (consPPR-DYW) protein, a representative of the PPR-DYW proteins, in both RNA-free and target RNA-bound states. Comparison between these states demonstrates domain movements upon target RNA binding, whereby the PPR domain accommodates the upstream sequence of the target C base in the proper conformation for editing while the DYW domain is optimally positioned for precise C-to-U conversion. These results, combined with comprehensive biochemical analyses, provide the foundation for a mechanistic model that explains the coordinated action of the PPR and DYW domains in achieving precise C-to-U editing.

CRISPR base editors enable scalable targeted DNA mutagenesis and are a powerful tool for analysing the function of variants of uncertain significance and disease modelling. Existing guide RNA (gRNA) design tools lack comprehensive functional annotation of target sequences. Here we developed BEstimate, a flexible computational pipeline that systematically specifies base editor gRNA target sites, generates on-target activity and off-target predictions, and provides functional, structural and clinical annotations of installed variants. BEstimate supports custom gRNA design against variant alleles and reversion of disease variants. BEstimate is a freely available, versatile tool for designing gRNA libraries and analysing base editor screens.

CRISPR-Cas12a is a versatile RNA-guided nuclease that has rapidly gained prominence for its dual functionality in genome editing and nucleic acid detection. In this Review, we discuss the structural, biochemical and mechanistic features of Cas12a that underpin its autonomous processing of the guide RNA and indiscriminate cleavage of single-stranded DNA, which enable Cas12a applications ranging from gene therapy to rapid diagnostics. We discuss key allosteric regulators and functional modules that orchestrate Cas12a activity, focusing on the core regulatory structural elements that control maturation of the guide RNA, target specificity, and both cis-cleavage and trans-cleavage activities, including the determinants of off-target cleavage. We provide a comparative analysis of Cas12a and the widely used Cas9, which further illuminates the distinctive attributes of Cas12a, and discuss recent advances in the characterization of its orthologues and in the development of engineered variants that expand its capabilities. Collectively, we present a comprehensive understanding of Cas12a and its increasing impact on biotechnology, therapeutics and molecular diagnostics.

Gene expression is regulated at multiple levels beyond genetic and epigenetic modifications of DNA. Even when DNA is accurately transcribed into RNA, transcript abundance often does not correlate with protein levels, underscoring the importance of posttranscriptional regulation. Chemical modifications of RNA occur in both coding and noncoding RNAs and add an additional layer of gene control. More than 170 distinct RNA modifications have been identified across different RNAs in all domains of life. Although the abundant modifications have been investigated, their roles in cardiac biology and heart failure remain incompletely defined. This review discusses the current knowledge of both well characterized and understudied RNA modifications in the heart. Recent studies highlight context-dependent roles of N6-methyladenosine (m6A), 5-methylcytosine (m5C), N4-acetylcytidine (ac4C), and adenosine-to-inosine (A-to-I) RNA editing in the heart are discussed in this review. RNA modifications constitute a critical regulatory layer that complements transcriptional control and facilitates rapid adaptation to cardiac stress. Dysregulation of m6A, m5C, and A-to-I editing contributes to pathological remodeling and disease progression. However, most RNA modifications remain unexplored in heart failure. Enzymes that write, erase, or read these marks represent promising targets for precision therapeutic strategies.

The Roridulaceae-Sarraceniaceae (RS) clade within Ericales exhibits strikingly divergent carnivorous strategies. To investigate how these differences shape plastid genome (plastome) evolution, we analyzed four representative species: