bims-mirnam Biomed News
on Mitochondrial RNA metabolism
Issue of 2026–05–10
seven papers selected by
Hana Antonicka, McGill University
  1. Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.
  2. Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing.
  3. When membrane insertion sets the pace of mitochondrial translation.
  4. The Expanding Landscape of ADP-Ribosylation: Protein, DNA, RNA, and Mitochondrial Regulation.
  5. Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed.
  6. RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.
  7. Mitochondrial RNA helicase DDX28 promotes cell cycle and DNA repair programs and shapes an immunosuppressive microenvironment in acute myeloid leukemia.
  1. Genome Biol. 2026 May 07.
    Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.
    Neda Ghohabi Esfahani, Andrew J Stein, Stuart Akeson, Talia Tzadikario, Connor Powell, Pooria Daneshvar Kakhaki, Miten Jain.
       BACKGROUND: Nanopore technology enables the direct sequencing of intact RNA molecules allowing for the detection of native chemical modifications. In 2024, Oxford Nanopore Technologies updated direct RNA sequencing from RNA002 to RNA004 platform as well as releasing an improved basecaller (Dorado) capable of de novo detection of eight RNA modifications. We compare RNA002 and RNA004 platforms for poly(A) RNA from GM12878 and HEK293 cell lines and evaluate Dorado-based RNA modification calling.
    RESULTS: We compute U-to-C mismatches, previously used to identify putative pseudouridine sites, and run m6anet for identifying putative N6-methyladenosine sites. We find that Dorado identifies global and site-specific differences when compared to RNA002 methods. We examine eight RNA modifications detected by Dorado for Nanopore direct RNA sequencing data and propose an analysis strategy for curating RNA modification predictions, including thresholds for read coverage and modification occupancy, canonical RNA-based false positive correction, and comparison with orthogonal information. When comparing modification sites called by Dorado versus those documented by orthogonal datasets, we note significant discordance and we document disagreements between our results and orthogonal datasets.
    CONCLUSIONS: The transition from RNA002 to RNA004 substantially improves sequencing accuracy and modification calling. However, Nanopore direct RNA sequencing-based RNA modification detection requires careful validation. We recommend combining Nanopore direct RNA sequencing with orthogonal methods and appropriate filtering strategies for increased confidence in modification calls.
    Keywords:  Direct RNA sequencing; Modification calling performance; Nanopore sequencing; RNA modification
    DOI:  https://doi.org/10.1186/s13059-026-04096-w
  2. Nucleic Acids Res. 2026 Apr 23. pii: gkag411. [Epub ahead of print]54(8):
    Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing.
    Xinqi Kang, Kelly Zhang, Alexandre Goyon, William Stephenson.
      While nanopore direct RNA sequencing has substantially advanced transcriptomics, its detection of RNA modifications remains primarily focused on abundant biological base modifications. However, therapeutic RNAs employ a diverse catalog of modifications, including base, sugar, and backbone modifications, to enhance stability and pharmacological properties. To address this gap, we systematically evaluated a set of therapeutically relevant modifications [phosphorothioate (PS)], sugar [2'-O-methylation (2'OMe), 2'-Fluoro (2'F), locked nucleic acid (LNA), 2'-O-(2'-methoxyethyl) (2'MOE)], and base [N1-methylpseudouridine (m1Ψ), 5-methylcytidine (m5C), 5-methoxyuridine (5moU), and 5-iodocytidine (5iodoC)] using direct RNA nanopore sequencing. Modifications were systematically analyzed using basecall errors, raw current signals, and modification-aware basecalling models. Ribose modifications, m1Ψ, and 5moU induced significant error rate increases and noticeable current alterations, whereas 2'OMe and 2'MOE affected dwell time adjacent to the pore. In contrast, PS linkages produced only slight current alterations without increasing basecalling errors. We further evaluated modification-aware basecallers for 2'OMe and m5C. While these tools can distinguish modification types, they are limited by poor quantification accuracy and high local error rates, especially for 2'OMe. This study establishes a critical performance baseline, clarifying the current capability and limitations of nanopore technology for the analysis of therapeutically relevant RNA modifications.
    DOI:  https://doi.org/10.1093/nar/gkag411
  3. Nat Struct Mol Biol. 2026 May 07.
    When membrane insertion sets the pace of mitochondrial translation.
    Michele Brischigliaro, Antoni Barrientos.
      
    DOI:  https://doi.org/10.1038/s41594-026-01799-3
  4. Chem Res Toxicol. 2026 May 04.
    The Expanding Landscape of ADP-Ribosylation: Protein, DNA, RNA, and Mitochondrial Regulation.
    Yi-Cheng Sin, Linlin Zhao.
      ADP-ribosylation is an essential post-translational modification that contributes to key cellular processes, such as DNA damage repair, cell-cycle progression, chromatin remodeling, mitochondrial function, and immune responses in mammalian cells. This modification derives from NAD+ and is regulated by dedicated writer, eraser, and reader proteins that govern its installation, removal, and recognition. Traditionally viewed as a protein-centered modification, ADP-ribosylation has recently been extended to nucleic acids, with ADP-ribosylated DNA and RNA now identified in both mammalian and bacterial systems. These discoveries reveal previously underappreciated layers of nucleic acid-based regulation and suggest that NAD+-dependent chemistry integrates genome maintenance, RNA metabolism, and cellular stress responses. In this review, we first outline the major mammalian ADP-ribosylation machineries, including the families of writer, eraser, and reader proteins, and discuss how their activities are coordinated. We then examine emerging roles of ADP-ribosylation in mitochondria, with a focus on mitochondrial DNA repair and metabolic control. Finally, we highlight recent advances in understanding NAD+-dependent modifications of DNA and RNA in mammalian and bacterial cells, including terminal and nucleobase-linked ADP-ribosylation and NAD capping, and discuss outstanding questions regarding their physiological functions and interplay with protein post-translational modification and other nucleic acid modifications.
    DOI:  https://doi.org/10.1021/acs.chemrestox.6c00176
  5. Nat Struct Mol Biol. 2026 May 07.
    Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed.
    Thomas Schöndorf, Valentyn Petrychenko, Ilgin Kotan, Drishan Dahal, Natalia Napieraj, Luis Daniel Cruz-Zaragoza, Cong Wang, Oliver Urbach, Tanja Gall, Sven Dennerlein, Günter Kramer, Niels Fischer, Peter Rehling.
      The human mitochondrial genome encodes 13 subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of 11 mRNAs by membrane-bound ribosomes is coupled to insertion of the nascent polypeptides into the inner membrane aided by the OXA1L insertase. To this end, the mechanism of membrane insertion of nascent polypeptides and the functional link to the translation process are not sufficiently understood. Here, we applied ribosome profiling to assess translation dynamics in combination with cryo-electron microscopy analysis of a COX1 ribosome-nascent chain complex to visualize cotranslational folding of the nascent chain. We find that the membrane topology of the translation product impacts translation speed and that positioning of amphipathic helices in the ribosome vestibule induces structural changes, correlating with translation pausing events. Thus, our findings reveal a link between translation process and folding and membrane insertion of nascent polypeptides at the inner mitochondrial membrane.
    DOI:  https://doi.org/10.1038/s41594-026-01803-w
  6. NAR Genom Bioinform. 2026 Jun;8(2): lqag044
    RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.
    Abdelraouf O Dapour, Jacopo Manigrasso, Warren B Rouse, Giuseppina La Sala, Miles V Aronnax, Leonardo De Maria, Russell S Hamilton, Sergio Martinez Cuesta, Anders Hogner, Walter N Moss.
      RNA structure critically governs biological function in both physiological and pathological contexts, making high-resolution structural maps essential for RNA-targeted therapeutics. Yet, despite recent advances, well-validated structural targets for drug design remain limited. To help bridge this gap, we generated the first genome-scale map of the human RNA structurome by applying ScanFold to >230 000 annotated human pre-mRNA transcripts, identifying sequences likely evolved to form highly stable and functional secondary structures. We also performed a global analysis of regions with z-scores ≤ -2 and statistically characterized their two-dimensional folding patterns. In addition, we developed the RNA-Annotator Pipeline to integrate 20 diverse biological annotations, such as tissue-specific expression and protein interactions, with the structural data. Our results reveal local folding propensities and unusually stable structures with high-confidence architectures, providing insights for prioritizing RNA targets and guiding therapeutic design, including antisense oligonucleotides and small molecules. All ScanFold results are publicly available through RNAStructuromeDB. Using the RNA-Annotator Pipeline, analysis of SMN1 and SMN2 pre-mRNAs showed that a single C-to-T transition in SMN2 induces structural rearrangements that disrupt a critical splicing enhancer. This toolkit establishes an integrated workflow that enables researchers to explore RNA structure-function relationships and accelerate advances in RNA-targeted drug discovery and RNA biology.
    DOI:  https://doi.org/10.1093/nargab/lqag044
  7. Transl Oncol. 2026 May 05. pii: S1936-5233(26)00103-8. [Epub ahead of print]69 102766
    Mitochondrial RNA helicase DDX28 promotes cell cycle and DNA repair programs and shapes an immunosuppressive microenvironment in acute myeloid leukemia.
    Zi Wang, Yunli Liu, Xinzhu Guan, Miaoqing Ye, Xinxin Xu.
      Acute myeloid leukemia (AML) is a heterogeneous malignancy with frequent relapse, driven by intertwined alterations in mitochondrial function, cell cycle control, genome maintenance, and immune evasion. DDX28 is a mitochondrial DEAD-box RNA helicase required for mitoribosome assembly and mitochondrial translation, and has been implicated in bioenergetic regulation in other tumor contexts. Here, we profiled DDX28 expression across AML cohorts using integrated multi-omics resources and evaluated its associations with prognosis, immune microenvironment features, and predicted drug response. Functional annotation, pathway analysis, GSEA, and targeted in vitro assays were used to explore potential mechanisms. High DDX28 expression was associated with inferior survival and higher blast burden. Mechanistically, elevated DDX28 expression was linked to promoter hypomethylation and was positively correlated with the transcription factor THAP11. Transcriptomic signatures in the high DDX28 group were enriched for cell cycle progression and DNA damage repair programs, together with an immune-suppressive landscape characterized by increased regulatory T cells and M2 macrophage signatures. Single-cell RNA-seq analyses further showed DDX28 enrichment in malignant blasts and exhausted or proliferative T-cell states. Consistently, DDX28 knockdown by siRNA in HEL cells reduced proliferation and impaired migration and invasion. Although direct metabolic flux measurements were not performed, the mitochondrial localization of DDX28 and the enrichment of proliferation and repair programs support a model in which DDX28 couples mitochondrial translation with the biosynthetic and genome maintenance demands of rapidly cycling AML cells. Collectively, our findings identify DDX28 as a prognostic indicator and a candidate regulator of malignant and immune states in AML, with potential relevance to therapeutic response.
    Keywords:  Acute myeloid leukemia; Bioinformatic analysis; DDX28; Immune microenvironment; Prognostic biomarker
    DOI:  https://doi.org/10.1016/j.tranon.2026.102766
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