bims-mirnam Biomed News
on Mitochondrial RNA metabolism
Issue of 2026–01–18
twelve papers selected by
Hana Antonicka, McGill University
  1. Mrx6 binds the Lon protease Pim1 N-terminal domain to confer selective substrate specificity and regulate mtDNA copy number.
  2. Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells.
  3. CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.
  4. Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.
  5. Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.
  6. The nuclear and mitochondrial genomes need to tango. How is their dance synchronized during development?
  7. Bridging single-molecule and genome-wide studies of cellular mRNA translation.
  8. A central role for PINK1 in governing local mitochondrial biogenesis and degradation in neurons.
  9. Structural analysis of uridine modifications in solved RNA structures.
  10. Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.
  11. RNA-binding proteins and ribonucleoproteins as determinants of immunity.
  12. tRNA synthetase activity is required for stress granule and P-body assembly.
  1. Nucleic Acids Res. 2026 Jan 14. pii: gkaf1390. [Epub ahead of print]54(2):
    Mrx6 binds the Lon protease Pim1 N-terminal domain to confer selective substrate specificity and regulate mtDNA copy number.
    Simon Schrott, Ilaria Marafelli, Charlotte Gerle, Sebastian Bibinger, Lea Bertgen, Giada Marino, Serena Schwenkert, Romina Rathberger, Johannes M Herrmann, Christof Osman.
      Mitochondrial DNA (mtDNA) copy number regulation remains incompletely understood, despite its importance in cellular function. In Saccharomyces cerevisiae, Mrx6 belongs to the Pet20-domain-containing protein family, consisting of Mrx6, Pet20, and Sue1. Notably, absence of Mrx6 leads to increased mtDNA copy number. Here, we identify the C-terminus of Mrx6 as essential for its stability and interaction with the mitochondrial matrix protein Mam33. Deletion of Mam33 mimics the effect of Mrx6 loss, resulting in elevated mtDNA copy number. Bioinformatics, mutational analyses, and immunoprecipitation studies corroborate that a subcomplex of Mam33 and Mrx6 trimers interacts with the substrate recognition domain of the conserved mitochondrial Lon protease Pim1 through a bipartite domain in the Pet20 domain of Mrx6. Loss of Mrx6, its paralog Pet20, Mam33, or mutations disrupting the interaction between Mrx6 and Pim1 stabilize key proteins required for mtDNA maintenance, the RNA polymerase Rpo41 and the HMG-box-containing protein Cim1. We propose that Mrx6, alongside Pet20 and Mam33, regulates mtDNA copy number by modulating substrate degradation through Pim1. Additionally, Mrx6 loss alters Cim1's function, preventing the detrimental effect on mtDNA maintenance observed upon Cim1 overexpression. The presence of three Pet20-domain proteins in yeast implies broader roles of Lon protease substrate recognition beyond mtDNA regulation.
    DOI:  https://doi.org/10.1093/nar/gkaf1390
  2. bioRxiv. 2026 Jan 07. pii: 2026.01.06.698062. [Epub ahead of print]
    Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells.
    Abby R Thurm, Tanya H Nguyen, Jesus Damian Torres Campos, Matthew Mansfield, Lacramioara Bintu, Lauren D Hagler.
      RNA structures that form inside living cells influence processes ranging from translation to RNA decay, many of which are controlled by RNA-binding proteins (RBPs). Because RBP specificity depends on both local RNA structure and sequence motifs, traditional pulldown-based methods often obscure the structural context of bound RNAs. Here, a quantitative framework based on dimethyl sulfate mutational profiling and sequencing (DMS-MaPseq) is introduced that jointly measures RNA structure and protein binding at single-nucleotide resolution in human cells, enabling estimation of effective RNA-protein affinities and fractional occupancy directly in cells. Application of this approach to a 1,600-member library of MS2 hairpin mutants reveals that RNA folding is the strongest determinant of MS2 coat protein (MCP) recognition, and that stable MS2 structures must form for MCP to bind its target sequence. MCP also shows strong preference for its consensus loop sequence while displaying minimal dependence on stem length beyond ten base pairs or on stem GC content. Incorporation of an inducible degron fused to MCP allows precise tuning of intracellular protein concentrations analogous to those of many endogenous RBPs and show that DMS reactivity changes can be used to infer binding specificities across a subsaturating regime. A quantitative occupancy framework further shows that inferred fraction-bound values accurately predict how efficiently MCP fused to a downregulatory-domain drives RNA degradation. Together, these results establish a generalizable approach for measuring RBP-RNA affinities with structural resolution in living cells, dissecting how sequence and structure contribute to RBP recognition, and quantitatively linking occupancy to functional output.
    DOI:  https://doi.org/10.64898/2026.01.06.698062
  3. Brief Bioinform. 2026 Jan 07. pii: bbaf726. [Epub ahead of print]27(1):
    CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.
    Jiayi Li, Shenglun Chen, Zhixing Wu, Haozhe Wang, Rong Xia, Jia Meng, Yuxin Zhang.
      Circular RNA (circRNA) represents a critical class of regulatory RNAs with distinctive structural and functional features. The functions of circRNAs are modulated by various RNA modifications. Here, we present CircRM, a nanopore direct RNA sequencing-based computational method for profiling RNA modifications in circRNAs at single-base and single-molecule resolution. By integrating circRNA detection, read-level modification detection, and quantitative assessment of methylation rates, CircRM identified 427 high-confidence circRNAs and enables systematic characterization of three major modifications, m5C (AUC = 0.855), m6A (AUC = 0.817) and m1A (AUC = 0.769). It revealed distinct modification patterns compared with linear RNAs, highlighting RNA-type-specific regulations. We also identified the key features of circRNA-specific modifications, such as the enrichment near the back-splice junctions. Cross-cell line analyses further demonstrated conserved and cell-type-specific modification patterns. Together, these findings reveal, at the computational level, a unique epitranscriptomic landscape associated with circRNAs and establish CircRM as a powerful tool for advancing the study of RNA modifications in circular RNA biology. CircRM is free accessible at: https://github.com/jiayiAnnie17/CircRM.
    Keywords:  circular RNA; epitranscriptomics; nanopore direct RNA sequencing
    DOI:  https://doi.org/10.1093/bib/bbaf726
  4. Nat Commun. 2026 Jan 14.
    Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.
    Han Dong, Yongsheng Gao, Zhengyi Cai, Yi Li, Xing Li, Fangqing Zhao, Jinyang Zhang.
      Despite the extensive studies of individual RNA modifications, the lack of methods to detect multiple modification types simultaneously has left the global epitranscriptomic landscape and its underlying crosstalk largely unexplored. Here, we present ORCA (Omni-RNA modification Characterization and Annotation), a deep learning framework that enables comprehensive mapping of RNA modification landscape using nanopore direct RNA sequencing. ORCA employs domain adversarial learning to detect and quantify a wide range of modifications by leveraging mixed stoichiometry-driven signal and sequence variability between modified and unmodified nucleotides. It also incorporates a transfer learning module for accurate annotation of modification types with minimal prior knowledge. Applying ORCA to multiple human cell lines reveals widespread, isoform-specific modification patterns, as well as intricate cooperative and competitive interactions among neighboring modification sites. This approach substantially expands the repertoire of known RNA modification sites and elucidates their spatial organization, revealing the emerging roles of RNA modifications in splicing regulation. ORCA thus provides an unbiased and generalizable framework for decoding RNA modification dynamics and their regulatory complexity across diverse biological contexts.
    DOI:  https://doi.org/10.1038/s41467-026-68419-y
  5. RNA. 2026 Jan 14. pii: rna.080908.125. [Epub ahead of print]
    Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.
    Aaron M Fleming, Cynthia J Burrows.
      Nanopore direct RNA sequencing (DRS) is revolutionizing our ability to analyze the epitranscriptome to evaluate nucleoside modifications in both cellular and synthetic RNA. The process involves minimal handling of fragile RNA strands, one round of reverse transcription to provide a DNA:RNA duplex, and library preparation to directly read nucleotides with their modifications as the pass through a protein nanopore embedded in a membrane. Simultaneous sequencing of hundreds of strands on a chip provides unprecedented access to whole transcriptome information. A key advantage is the long read length that permits, for example, operon-specific epitranscriptomics of ribosomal RNA modifications as a function of cellular stress. By analyzing the entire transcriptome, the interplay of different modifications on the same RNA, or the correlation of changes in different RNAs in the same cell type can be monitored. This review presents several recent examples of the types of experiments that are suitable for nanopore DRS as well as some of the current challenges and future expectations.
    Keywords:  Epitranscriptomics; Nanopore sequence; RNA modifications; Ribosomal RNA
    DOI:  https://doi.org/10.1261/rna.080908.125
  6. NAR Mol Med. 2026 Jan;3(1): ugaf042
    The nuclear and mitochondrial genomes need to tango. How is their dance synchronized during development?
    Justin C St John.
      For quite some time, knowledge about mitochondria and the mitochondrial genome has been primarily limited to energy production. However, there is now increasing evidence that they have many important roles in cell function and that synergy between the nuclear and mitochondrial genomes is an essential prerequisite to developmental outcome. This review describes the mitochondrial genome and its contribution to overall cellular genomic content; and discusses mitochondrial DNA (mtDNA) inheritance. mtDNA homoplasmy and heteroplasmy are defined and distinctions between pathogenic and non-pathogenic rearrangements are drawn; how they are transmitted; and their effects on oocyte quality and developmental outcomes. This is followed by analysis of mtDNA replication and changes in mtDNA copy number during development; why they need to happen; and how they influence developmental outcomes. Changes to nuclear DNA methylation events are then discussed in the context of changes to mtDNA replication throughout development. This leads to the concept of 'genomic balance', which defines how cells at any stage of development require adjustments to both genomes to ensure successful cellular function and development; and how this process can be perturbed by some of the more invasive assisted reproductive technologies designed to treat infertility and mtDNA disease.
    DOI:  https://doi.org/10.1093/narmme/ugaf042
  7. RNA. 2026 Jan 12. pii: rna.080824.125. [Epub ahead of print]
    Bridging single-molecule and genome-wide studies of cellular mRNA translation.
    Adam Koch, Kotaro Tomuro, Taisei Wakigawa, Tatsuya Morisaki, Shintaro J Iwasaki, Timothy J Stasevich.
      The translation of mRNA is a tightly regulated, energy-intensive process that drives cellular diversity. Understanding its control requires tools that can capture behavior across scales. Over the past two decades, two complementary techniques have emerged that have transformed our understanding of mRNA translation within cells: ribosome profiling (Ribo-Seq) and live, single-molecule imaging. Ribo-Seq provides genome-wide, codon-level maps of ribosome positions, revealing pause sites, novel open reading frames, and global translation efficiencies. In contrast, live, single-molecule imaging visualizes translation on individual mRNAs in living cells, uncovering heterogeneous initiation, elongation, pausing, and spatial organization in real time. Together, these methods offer complementary strengths - molecular breadth versus temporal and spatial precision - but are rarely applied in tandem. Here, we review their principles, key discoveries, and recent innovations that are bringing them closer together, including endogenous tagging, higher-throughput imaging, absolute calibration, and spatially resolved footprinting. Integrating these approaches promises a unified, multiscale view of translation that connects the dynamics of individual ribosomes to genome-wide patterns of protein synthesis.
    DOI:  https://doi.org/10.1261/rna.080824.125
  8. Cell Mol Life Sci. 2026 Jan 12.
    A central role for PINK1 in governing local mitochondrial biogenesis and degradation in neurons.
    Marlena Helms, Angelika B Harbauer.
      Neurons have adapted the transport and positioning of mitochondria to fit their extended shape and high energy needs. To sustain mitochondrial function, neurons developed systems that allow local biogenesis and adaption to locally regulate mitochondrial form and function. Likewise, fine-tuned degradative systems are required to protect the neurons from mitochondrial dysfunction. Throughout both domains of mitostasis, the local synthesis of the mitochondrial damage-induced kinase PINK1 emerges as a central player. Along with other nuclear encoded mitochondrial proteins, its mRNA associates with mitochondria to sustain mitochondrial function locally. It also regulates mitochondrial degradation, via regulation of proteases, the generation of mitochondria-derived vesicles and mitophagy. In this review, we provide a general overview of the mechanisms governing mitochondrial health in neurons, with a special focus on the role of PINK1 in this endeavor.
    Keywords:  Local translation; Mitochondrial proteases; Mitophagy; mRNA transport
    DOI:  https://doi.org/10.1007/s00018-025-06054-4
  9. NAR Genom Bioinform. 2026 Mar;8(1): lqaf197
    Structural analysis of uridine modifications in solved RNA structures.
    Sebastian J Arteaga, Brent M Znosko.
      Naturally occurring uridine modifications in RNA play critical roles in modulating RNA stability, translation, and immune responses. While detection methods have advanced, a comprehensive structural analysis across experimentally determined RNA 3D structures remains limited. In this study, we systematically examined six uridine modifications-pseudouridine (PSU), 5-methyluridine (5MU), 3-methyluridine (UR3), O2'-methyluridine (OMU), 4-thiouridine (4SU), and 5,6-dihydrouridine (H2U)-using data from the Research Collaboratory for Structural Bioinformatics Protein Data Bank. After curation, we identified 2982 PSU, 736 5MU, 232 UR3, 429 OMU, 314 4SU, and 171 H2U residues across RNA-containing structures. These modifications were primarily found in ribosomal and transfer RNAs, often localized within hairpin secondary structures. Sugar pucker analysis revealed modification-specific preferences for C3'-endo and C2'-endo conformations. To assess structural impacts, we generated sequence-representative structures and compared modified versus unmodified forms using all-atom root-mean-square deviation analysis. Most modifications showed high similarity to their unmodified counterparts (RMSD [Formula: see text] 1.0 Å), though deviations were notable for certain PSU-, 5MU-, and 4SU-containing motifs. Despite overall similarity, interaction differences were observed between modified and canonical uridines. This work provides a detailed structural overview of uridine modifications, offering insights into their conformational behavior and implications for RNA function. These findings may inform future efforts in RNA-targeted therapeutics and structural biology.
    DOI:  https://doi.org/10.1093/nargab/lqaf197
  10. RNA. 2026 Jan 14. pii: rna.080830.125. [Epub ahead of print]
    Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.
    Zhuoyi Song, Eric L Van Nostrand.
      RNA binding proteins (RBPs) play essential roles in post-transcriptional gene regulation by interacting with a wide range of RNA targets. In addition to regulating RNA processing via individual RBP-RNA interactions, there is a growing appreciation of the regulatory impact of protein-associated RNA-RNA interactions that include both well-studied examples of small regulatory RNAs (e.g. microRNAs, snRNAs, snoRNAs, piRNAs) guiding ribonucleoprotein complexes to their targets as well as structured RNA elements defining the interaction landscape for an RBP. To elucidate the full scope of RBP-RNA interactions, CLIP ( crosslinking and immunoprecipitation)-based methods have emerged as powerful tools. Even with the wide application of CLIP and variant approaches, these methods are still under significant ongoing advancement to better accommodate diverse biological systems and experimental demands and improve scalability. In particular, recent years have seen an emergent focus on improved techniques to globally profile protein-associated RNA-RNA interactions. In this review, we provide a summary of recent improvements in traditional CLIP methods that improve the mapping of RBP-RNA interactions, with particular focus on those that specifically enable the profiling of protein-associated RNA-RNA interactions. We discuss the unique challenges involved in mapping protein-associated RNA-RNA interactions and highlight different ways current approaches address these challenges in order to offer a practical framework for researchers seeking to investigate RBP-associated RNA interactions.
    Keywords:  CLASH; CLIP; RNA interactions; RRI; chimeric CLIP
    DOI:  https://doi.org/10.1261/rna.080830.125
  11. Nat Rev Immunol. 2026 Jan 15.
    RNA-binding proteins and ribonucleoproteins as determinants of immunity.
    Martin Turner, Georg Petkau.
      Infection triggers one of the most dramatic systemic responses in the body, and the coordinated activation and function of immune cells requires a dynamic regulation of transcriptomes and proteomes. This is achieved by RNA-binding proteins, which, together with RNA, form ribonucleoproteins. These proteins expand the information content of the genome and determine the lifespan, localization and function of RNA. Moreover, they control when, where and how much protein is produced. They can also mediate cell-autonomous immunity to foreign RNA and to misfolded self-RNAs and ensure the fidelity of the transcriptome by acting as RNA modifiers and chaperones to prevent RNA misfolding. These activities are integrated with gene expression programmes that are induced by the pathogen-sensing mechanisms of immune cells, which together activate, and later resolve, immune responses. Here, we review the activities of RNA-binding proteins in immune cells and discuss how perturbations of their function can result in immunodeficiency, autoimmunity and chronic inflammation.
    DOI:  https://doi.org/10.1038/s41577-025-01254-2
  12. Genes Dev. 2026 Jan 14.
    tRNA synthetase activity is required for stress granule and P-body assembly.
    Max Baymiller, Noah S Helton, Benjamin Dodd, Stephanie L Moon.
      Translation elongation defects activate the integrated stress response (ISR), but whether and how ribosome stalls are cleared to enable mRNA release for ribonucleoprotein (RNP) granule assembly remain unclear. We show that blocking tRNA aminoacylation generates persistent uncollided ribosome stalls that inhibit stress granule and P-body assembly despite robust ISR activation. Collided ribosomes are rapidly cleared by ZNF598-dependent ribosome-associated quality control within 4 h, while uncollided stalls resist clearance and persist for >16 h. Puromycin releases persistent stalls and restores RNP granule formation. The block in stress granule assembly is generalizable across tRNA synthetase inhibitors and amino acid deprivation. Therefore, stress granules represent signal integrators reporting translation elongation status when initiation is suppressed. Our findings reveal that translation quality control pathways selectively clear collided ribosomes, establish that translation elongation stress uncouples RNP granule assembly from the ISR, and suggest that tolerating uncollided stalls may be adaptive for cotranslational processes essential for cellular function.
    Keywords:  P-bodies; halofuginone; integrated stress response; ribosome collisions; ribosome-associated quality control; stress granules; tRNA synthetase; translation elongation
    DOI:  https://doi.org/10.1101/gad.353535.125
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