bims-mirnam 2026-10-11 papers

Issue of 2026–10–11
five papers selected by
Hana Antonicka, McGill University

Angew Chem Int Ed Engl. 2026 Oct 06. e7655789

dsRADAR: Imaging and Detecting Cellular dsRNA by Repurposing RNA-Binding Proteins.

Weina Cheng, Tyson D Todd, Alexandria L Quillin, Harshad Ingle, Angela M Halstead, Megan T Baldridge, José B Sáenz, Jennifer M Heemstra.

Double-stranded RNA (dsRNA) is recognized by cellular receptors as a sign of viral infection, triggering the innate immune response. Cellular dysregulation can also lead to accumulation of endogenously produced dsRNA that stimulates a viral-like immune response. Additionally, dsRNA contamination in RNA therapeutics can lead to harmful side effects via a similar pathway. Despite the clinical relevance of dsRNA, reliable tools for its detection remain limited. Currently, dsRNA detection relies almost exclusively on the monoclonal antibodies J2 and K1, which suffer from sequence bias and low sensitivity. To address this challenge, we repurposed naturally occurring dsRNA-binding domains (dsRBDs) to produce reliable, pan-specific affinity reagents for dsRNA. We systematically screened the dsRBDs of the three human adenosine deaminases acting on RNA (ADARs) and identified ADAR3 dsRBDs as the most promising candidates. We then engineered ADAR3-derived dsRBD constructs having varying linker lengths and domain combinations to create dsRNA accumulation detected by ADAR3 RBDs (dsRADAR) affinity reagents. Finally, we demonstrate the superior performance of dsRADAR over currently available dsRNA antibodies in a cell model of viral infection and a tissue model of gastric inflammation. Together, dsRADAR provides a sensitive and reliable approach for imaging and detecting diverse dsRNA structures in biological contexts.

Keywords: RNA recognition; RNA structures; immunoassays

DOI: https://doi.org/10.1002/anie.7655789

Biochemistry (Mosc). 2026 Sep;91(9): 1481-1506

Roles of Mitochondrial Genome-Encoded Circular RNAs (mecciRNAs) in Human Diseases: Potential Biomarkers and Therapeutic Targets.

Zahra Firoozi, Abbas Shahi, Mohammadreza Sharifi, Ali Moravej, Saeed Mohammadi, Abdolreza Daraei, Hassan Dastsooz, Yaser Mansoori, Rasoul Salehi.

Generation of energy and maintenance of homeostasis in eukaryotic cells depends on organelles known as mitochondria, which have their own circular genomes and take part in a number of metabolic activities and cellular events. Bioinformatics techniques and RNA-sequencing (RNA-seq) have helped unravel intricacy of the transcripts originating from mitochondria. Numerous mitochondrial noncoding RNAs (mt-ncRNAs) have been identified in the recent studies, and they are crucial for both mitochondrial and other cellular processes. According to the recently published research, circular RNAs (circRNAs) are endogenous macromolecules with covalent closure at the 5' and 3' ends, which are one of the novel subtypes of ncRNAs. CircRNAs are mostly found in the cytoplasm and nucleus, although this kind of ncRNA can also be detected in mitochondria. Mitochondrial genome-encoded circular RNAs (mecciRNAs) play key roles in regulating cellular phenotypes and progressive illness by sponging microRNA (miRNA) and interacting with the RNA binding proteins (RBP). In this review, we focus on the recent research on the regulatory mechanism and possible functions of mecciRNAs in pathophysiology of various diseases.

Keywords: circRNAs; mecciRNAs; mitochondria; ncRNAs

DOI: https://doi.org/10.1134/S0006297926601668

Biomol NMR Assign. 2026 Oct 09. pii: 29. [Epub ahead of print]20(1):

1H, 13C, and 15N resonance assignments and solution structure of the first double-stranded RNA-binding domain of DExH-Box Helicase 30 (DHX30).

Chikage Abe, Yutaka Muto, Fahu He, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Güntert, Mikako Shirouzu, Shigeyuki Yokoyama, Kanako Kuwasako.

DHX30 is a member of the DExH-box helicase family and contains two double-stranded RNA-binding domains (dsRBDs) N-terminal to the helicase core domain. DHX30 plays a fundamental role in regulating the translation of transcripts encoding mitoribosomal proteins, thereby facilitating mitoribosome biogenesis. Additionally, DHX30 is involved in the formation of stress granules. These intracellular structures are composed of proteins and RNAs, including mRNAs, and form under stress conditions in association with translational repression. Recent studies have demonstrated that pathogenic mutations in DHX30 underlie a severe neurodevelopmental disorder termed neurodevelopmental disorder with variable motor and language impairment (NEDMIAL), possibly in part through aberrant stress-granule formation. Structural characterization of these RNA-binding domains is an important step toward understanding the molecular basis of DHX30 function. In this study, we focus on the first dsRBD (dsRBD-1) of human DHX30 and report its 1H, 13C, and 15N resonance assignments and solution structure. DHX30 dsRBD-1 adopts an α0-α1-α1'-β1-β2-β3-α2-α3 topology, with three additional helices (α0, α1', and α3) relative to the canonical dsRBD topology (α1-β1-β2-β3-α2). To our knowledge, this is the first experimentally determined structure of a DHX30 domain. These resonance assignments and structural insights provide a valuable foundation for future structural and functional studies of DHX30.

Keywords: DExH-box helicase 30 (DHX30); Mitochondrial ribosome biogenesis; NEDMIAL; dsRBD

DOI: https://doi.org/10.1007/s12104-026-10279-0

Arch Biochem Biophys. 2026 Oct 08. pii: S0003-9861(26)00293-6. [Epub ahead of print]786 111020

Probing transcript RNA G-quadruplexes using an engineered RHAU-RNase HI enzyme.

Khac Huy Ngo, Thao Thu Thi Nguyen, Dung Thanh Dang.

G-quadruplexes (G4s) in functional RNAs regulate telomere maintenance, mRNA processing, and disease pathways, but their detection in long transcripts is limited by biophysical methods. Herein, we engineered RHAU-RNase HI, fusing the G4-binding RHAU domain (aa 53-192) with RNase HI (Bacillus halodurans), to probe RNA G4s via enhanced RNA-DNA hybrid cleavage with antisense oligonucleotides (ASOs). The results showed RHAU-RNase HI fusion protein selectively binds G4-containing RNA (R1) while RNase HI alone showed no detectable binding. Both RHAU-RNase HI and RNase HI enzymes exhibited comparably low cleavage efficiencies toward G4-free RNA substrate (R2) under standardized condition. In contrast, RHAU-RNase HI exhibited approximately 4-fold greater cleavage activity than RNase HI toward the G4-containing RNA substrate (R1). In addition, RHAU-RNase HI exhibited approximately 8-fold higher cleavage efficiency at the G4-proximal site than the G4-distal site. Collectively, our results show that RHAU-RNase HI recognizes G4 structures and enhances the cleavage of RNA-DNA hybrids adjacent to G4 motifs. These findings highlight RHAU-RNase HI as a promising biochemical tool for G4 structure mapping in complex RNA sequences.

Keywords: ASO; G4 RNA; Probing; RHAU; RHAU-RNase HI

DOI: https://doi.org/10.1016/j.abb.2026.111020

Nucleic Acids Res. 2026 Sep 22. pii: gkag963. [Epub ahead of print]54(18):

MTERF1 polar roadblock mechanism revealed using high-throughput magnetic tweezers and accurate single-bead force calibration.

Pim P B America, Eugeniu Ostrofet, Britney Johnson, Salina Quack, Flavia Stal-Papini, Quinte Smitskamp, Daniel Buc, Jamie J Arnold, Craig E Cameron, David Dulin.

High-throughput force spectroscopy assays, such as with magnetic tweezers, enable reconstruction of biomolecular reaction energy landscapes and provide access to rare events with deep statistics. Accurate force calibration is essential for describing complex reactions, which can be hindered by sample heterogeneity, such as bead-to-bead differences in magnetic content. Here, we describe an in-situ force calibration methodology for high-throughput magnetic tweezers that enables the calibration for each individual bead with a precision of up to 3%, limited only by the statistical resolution. Using this approach, we investigated the mechanism of polar roadblocking by the mitochondrial transcription termination factor 1 (MTERF1) bound to the termination site. Establishing a SpyCatcher surface-attachment strategy, we performed force-jump experiments on the same tethers for up to 11 h. We showed that directional DNA unwinding is sufficient to explain the polar roadblock activity of MTERF1. Accurate force spectroscopy further reveals that the unlocking transition is rate-limited by a single kinetic barrier, with a transition-state distance consistent with structural interpretations. Together, these results provide a mechanistic and broadly applicable model for the asymmetric stability of MTERF1 and other nucleic acid polar roadblocks and establish a robust force spectroscopy framework for high-throughput magnetic tweezers experiments.

DOI: https://doi.org/10.1093/nar/gkag963