bims-mirnam 2026-03-01 papers

bims-mirnam

Biomed News

on Mitochondrial RNA metabolism

Issue of 2026–03–01
eleven papers selected by
Hana Antonicka, McGill University

Cooperative Architecture of Mitochondrial Proteome Homeostasis.
Specific SLC25 carriers regulate mitochondrial protein synthesis.
Decoding the dark genome reveals its organisation into modular disease networks.
Quantitative and Visual Detection of Pseudouridine at Specific Sites Using Bisulfite-Assisted Rolling Circle Amplification.
RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.
Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging.
Aging-associated mitochondrial circular RNAs.
Mitochondria-Associated MicroRNAs: Emerging Roles in the Pathogenesis of Parkinson's Disease.
A case report of combined oxidative phosphorylation deficiency 35 (COXPD35) in Palestine caused by novel compound heterozygous TRIT1 variants.
Reversible phosphorylation influences energetic cellular metabolism by modulating mitochondrial gene expression.
G-Quadruplex Unwinding Molecular Mechanisms by Helicases and Their Applications.

medRxiv. 2026 Feb 09. pii: 2026.02.06.26345691. [Epub ahead of print]

Cooperative Architecture of Mitochondrial Proteome Homeostasis.

Patrick Forny, Merima Forny, Andrew J Smith, Andrew Y Sung, Kaixian Liu, David J Pagliarini.

Mitochondria are semi-autonomous organelles whose generation and maintenance demand precise expression, processing, and assembly of >1,000 proteins encoded across two genomes. To explore this cooperativity, we performed multiomic analyses on >200 cell lines harboring mitochondrial gene perturbations, generating >26M molecular measurements. Our data reveal that mitochondrial proteome homeostasis is heavily influenced by post-transcriptional processes. Through nearest neighbor analyses, we reveal diverse protein activities undergirding this regulation, including MDH2's regulation of MT-ND3 transcription via FASTKD1 binding and CLPP's processing of the mitoribosomal assembly factor MALSU1, which we establish as a disease gene. Through entropy analysis, we reveal unexpectedly heterogeneous protein-level variability across complexes and use complexome profiling to identify new complex-specific membership, including C15orf61's association with complex V. We further observe substantial mtDNA copy number variation, notably upon disruption of the disease-related cobalamin biosynthesis protein MMADHC. Together, we establish new protein functions and provide a multilayered view into mitochondrial proteome regulation.
Highlights: Multiomic signatures across perturbations reveal extensive post-transcriptional regulationThe TCA cycle enzyme MDH2 binds FASTKD1 to modulate MT-ND3 transcript levelsMALSU1 is a CLPP protease substrate whose deficiency causes a mitochondrial diseaseC15orf61 binds ATP synthase and negatively regulates its higher order assemblyMMADHC inversely affects mtDNA levels potentially mediated through LONP1.

DOI: https://doi.org/10.64898/2026.02.06.26345691
Sci Adv. 2026 Feb 27. 12(9): eaeb0049

Specific SLC25 carriers regulate mitochondrial protein synthesis.

Danielle L Rudler, Laetitia A Hughes, Martin S King, Jessica Baker, Richard G Lee, Andrianto P Gandadireja, Anisha Sunil, Samuel V Fagan, Blake Payne, Nicola Gray, Tim McCubbin, Edmund R S Kunji, Oliver Rackham, Aleksandra Filipovska.

A genome-wide knockout screen identified members of the SLC25 family of mitochondrial carrier proteins as important regulators of the rate of de novo mitochondrial protein synthesis. To elucidate this relationship, we generated human cell knockouts for SLC25A25, SLC25A44, SLC25A45, and SLC25A48, which have been shown to exchange adenosine triphosphate-magnesium (ATP-Mg) and phosphate, branched-chain amino acids, methylated basic amino acids, and choline, respectively. Multiomic and functional analyses identified that these four carriers are crucial for mitochondrial translation, biogenesis and function of the oxidative phosphorylation system, as well as mitochondrial morphology. Thermostability screens showed that SLC25A48 is specifically stabilized by choline, and changes in the mitochondrial metabolome and lipidome indicated defects in choline biosynthetic pathways and remodeling of mitochondrial membranes, both consistent with SLC25A48 being a choline transporter. These results highlight the essential roles of specific SLC25 transporters in maintaining mitochondrial structure and function and show that impaired transport of branched-chain amino acids, methylated basic amino acids, ATP-Mg, and choline affects mitochondrial translation.

DOI: https://doi.org/10.1126/sciadv.aeb0049
Sci Rep. 2026 Feb 22.

Decoding the dark genome reveals its organisation into modular disease networks.

Doris Kafita, Kevin Dzobo, Panji Nkhoma, Musalula Sinkala.

  The biological functions and disease relevance of the 'dark genome'-over one-third of all protein-coding genes-remain largely unknown. Here, we use integrative network and functional analyses to construct a systems-level map of dark gene contributions to human genetic diseases. We identify 16 hub dark genes, including R3HDM2 and RPUSD4, that are central to disease networks and are overwhelmingly enriched for roles in mitochondrial protein synthesis. These hubs form modular networks connecting major inflammatory conditions like psoriasis and tuberculosis, driven by specific transcription factors. Furthermore, we demonstrate that the expression of these hubs is controlled in a tissue-specific manner by thousands of genetic variants (eQTLs), providing direct mechanistic links to phenotypes such as myocardial infarction and diabetes. Our results provide a functional landscape for the dark genome, revealing its critical role in mitochondrial pathways and presenting a rich resource of novel therapeutic targets.

Keywords:  Human Diseasome; Mitochondrial Function; Network Analysis; The Dark Genome; eQTLs

DOI:  https://doi.org/10.1038/s41598-026-40553-z
Anal Chem. 2026 Feb 26.

Quantitative and Visual Detection of Pseudouridine at Specific Sites Using Bisulfite-Assisted Rolling Circle Amplification.

Xiumin Liu, Jiehua Li, Xiaoyang Duan, Xin Fang, Xiaochen Xue, Shaoqing Han, Xiang Zhou, Yafen Wang.

Pseudouridine (Ψ) is a prevalent RNA modification whose site-resolved quantification is critical for understanding epitranscriptomic regulation. We present pseU-SCOPE, a ligation-assisted rolling circle amplification (RCA) assay that converts a bisulfite-derived Ψ signature into a padlock-probe ligation gate, enabling single-nucleotide resolution without qPCR. The workflow supports fluorescence and gel-based, naked-eye readouts following RCA and operates with low RNA input. We validate pseU-SCOPE on established Ψ sites across human rRNAs and mitochondrial tRNAs, generate calibration curves for absolute quantification, and estimate site stoichiometry. Applied to peripheral blood samples, the assay reveals elevated rRNA pseudouridylation in acute myeloid leukemia relative to healthy donors, suggesting disease relevance. Coupled with the deamination mediated by GLORI (glyoxal and nitrite-mediated deamination of unmethylated adenosines), this strategy is adaptable to other RNA modifications such as N6-methyladenosine (m6A). Together, pseU-SCOPE provides a simple, rapid, qPCR-free, and visual platform for site-specific detection and quantification of RNA modifications, facilitating functional studies and translational research.

DOI: https://doi.org/10.1021/acs.analchem.5c08088
Nucleic Acids Res. 2026 Feb 24. pii: gkag090. [Epub ahead of print]54(5):

RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

Riccardo Mosca, Carlos J Gallardo-Dodd, Qun Li, Christian Sommerauer, Justas Šidiškis, Jonas Nørskov Søndergaard, Claudia Kutter.

Over the past decade, thousands of putative human RNA-binding proteins (RBPs) have been identified, increasing the need for methods that define their RNA-binding capacities across diverse biological settings. Existing methods rely either on antibody-based in vivo capture (e.g. CLIP-seq), which depends on cross-linking efficiency and antibody availability, or on synthetic oligonucleotide-based assays (e.g. RNAcompete), which use artificial RNA substrates and cannot assess binding across the native transcriptome. To bridge this gap, we developed RNA affinity purification followed by sequencing (RAPseq), an in vitro method that profiles RBP-binding to native cellular RNA, enabling large-scale transcriptome-wide characterization of RNA-protein interactions without antibodies or synthetic probes. Using RAPseq, we characterized the RNA interactomes of 11 canonical RBPs and 26 non-canonical RBPs, and uncovered novel and specialized moonlighting RNA-binding activities. Applying RAPseq to vertebrate HUR proteins revealed recognition of a conserved RNA-binding motif but showed species-specific binding preferences. Profiling of five pathological IGF2BP family variants exhibited distinct gain- and loss-of-function binding patterns, with implications for cancer biology. Our combinatorial RBP-binding assay (co-RAPseq) uncovered cooperative RNA-binding by HUR and PTBP1, including de novo estimation of the optimal binding distance. Lastly, we introduce a modification-sensitive assay (mod-RAPseq) to distinguish between modification-dependent and -independent RNA-binding sites of YTHDF1 and YBX1. Overall, our simple, scalable, and versatile method enables exploration of complex RNA-protein interactions and the regulatory layers that shape post-transcriptional gene regulation.

DOI: https://doi.org/10.1093/nar/gkag090
Chem Biomed Imaging. 2026 Feb 23. 4(2): 130-143

Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging.

Zhe Ma, Kulsoom, Fu Wang.

  Endogenous RNAs orchestrate cellular processes through precise spatiotemporal regulation, and live-cell imaging of these molecules is essential for dissecting their roles in gene expression, disease progression, and cellular homeostasis. While traditional methods rely on exogenous labeling or fixation, fluorescent RNA aptamer-based sensors have emerged as transformative tools for visualizing endogenous RNAs in their native context. These sensors allow real-time tracking of mRNA localization, miRNA activity, and RNA-protein interactions with minimal disturbance. However, challenges such as the requirement for exogenous fluorogenic dyes, limited brightness, photostability, and target specificity in complex cellular environments hinder their wider application. This review provides a comprehensive overview of recent advances in fluorescent RNA aptamer-based sensors, discussing the design principles, mechanisms of fluorescence activation, and their application in live-cell RNA imaging. We also address the current limitations and future directions for improving these sensors, highlighting their transformative potential in RNA biology and their implications for diagnostic and therapeutic strategies.

Keywords:  Biosensors; Fluorogenic Dyes; Imaging; RNA Aptamers; RNA Dynamics

DOI:  https://doi.org/10.1021/cbmi.5c00068
Aging (Albany NY). 2026 Feb 10. 18(1): 30-44

Aging-associated mitochondrial circular RNAs.

Hyejin Mun, Do-Won Ham, Nam Chul Kim, Bo-In Kwon, Young-Kook Kim, Je-Hyun Yoon.

  During mammalian aging, there are changes in abundance of noncoding RNAs including microRNAs, long noncoding RNAs, and circular RNAs. Although global profiles of the human transcriptome and epitranscriptome during the aging process are available, the existence and function of mitochondrial circular RNAs originating from the mitochondrial genome are poorly studied. Here, we report profiles of circular RNAs annotated to mitochondrial chromosome, chrM, in young and old cohorts. The most abundant circular RNA junctions are found in MT-RNR2, whose level is depleted in old cohorts and senescent fibroblast. The mitochondria-localized RNA-binding protein GRSF1 binds various mitochondrial transcripts, including linear and circular MT-RNR2, with a distinct RNA motif. Linear and circular MT-RNR2 bind a subset of TCA cycle enzymes, suggesting their possible function in regulating glucose metabolism in mitochondria to preserve proliferating status in young cohorts. In human fibroblasts, depletion of GRSF1 reduced levels of circMT-RNR2 and fumarate/succinate, concomitantly accelerating cellular senescence and mitochondrial dysfunction. Taken together, our findings demonstrate the existence and possible function of circular MT-RNR2 during human aging and senescence, implicating its role in promoting the TCA cycle.

Keywords:  GRSF1; MT-RNR2; TCA cycle; aging; circular RNA

DOI:  https://doi.org/10.18632/aging.206354
Biomedicines. 2026 Jan 30. pii: 313. [Epub ahead of print]14(2):

Mitochondria-Associated MicroRNAs: Emerging Roles in the Pathogenesis of Parkinson's Disease.

Mariano Catanesi, Luana Di Leandro, Martina Colasante, Annamaria Cimini, Michele D'Angelo, Vanessa Castelli, Cosmin Marian Obreja, Rodolfo Ippoliti.

  Neurodegenerative diseases (NDs) are the most prevalent age-associated disorders, characterized by progressive neuronal loss and cognitive decline. Mitochondrial dysfunction is strictly associated with NDs and represent one of the hallmarks of these disorders, with neurological syndromes frequently representing the primary clinical manifestations of mitochondrial abnormalities. As central regulators of cellular bioenergetics, mitochondria play a pivotal role in both the physiological maintenance and pathogenesis of disease by different regulatory approaches. One of these, microRNAs (miRNAs), a class of small non-coding RNAs, are well-established regulators of gene expression across different biological pathways. These miRNAs were usually investigated within the cytoplasmic context, but recent discoveries have revealed the presence of these miRNAs in different parts of mitochondria, where they contribute to the regulation of gene expression and metabolic activity. These mitochondrial-localized miRNAs, termed mito-MiRNA, may originate from either nuclear or mitochondrial genomes and have been shown to modulate the translational machinery of the cells. Despite extensive research on cytoplasmic miRNAs, the functional roles of mito-MiRNA remain poorly understood, particularly in the context of neurodegenerative disorders. Based on these findings, this review aims to synthesize emerging evidence on the involvement of mito-MiRNA in in one of most prevalent neurodegenerative diseases-Parkinson's disease (PD).

Keywords:  MiRNAs; Mito-MiRNA; Parkinson’s disease; agomir; antagomir; mitochondrial dysfunction

DOI:  https://doi.org/10.3390/biomedicines14020313
Medicine (Baltimore). 2026 Feb 27. 105(9): e47885

A case report of combined oxidative phosphorylation deficiency 35 (COXPD35) in Palestine caused by novel compound heterozygous TRIT1 variants.

Ali A A Doudin, Weam N I Omran, Saja M Alkomi, Ahmad Rjoub, Hamza Shoubaki, Shurooq Tayseer Abu Mufreh.

   RATIONALE: Combined oxidative phosphorylation deficiency 35 (COXPD35) is an extremely rare mitochondrial disorder inherited in an autosomal recessive pattern. It results from pathogenic variants in the TRIT1 gene, leading to hypomodified cytosolic and mitochondrial tRNAs. We report the first identified case of COXPD35 in Palestine, resulting from 2 novel variants of the TRIT1 gene.
PATIENT CONCERNS: A 2-year-and-6-month-old female patient with seizures, neurodevelopmental delay, microcephaly, dysmorphic facial features, abnormal electroencephalogram (EEG), and thinning of the corpus callosum on Brain magnetic resonance imaging, presenting to the Emergency Department with status epilepticus, and right lower lobe pneumonia.
DIAGNOSES: Combined oxidative phosphorylation deficiency 35 (COXPD35) caused by 2 novel TRIT1 variants that have never been previously reported in the literature, diagnosed clinically, and were identified by Whole-exome sequencing (WES) and confirmed by Sanger sequencing.
INTERVENTIONS: The patient received 1 shot of IV diazepam 0.3 mg/kg after IV cannulation, followed by IV ceftriaxone 500 mg twice daily, IV hydrocortisone 20 mg every 4 hours, and albuterol, ipratropium bromide, and hypertonic saline nebulizers regularly. Additionally, she was given intravenous fluids at a rate of 60 mL/h of 5% dextrose saline. She was given a 200 mg dose of phenytoin IV for seizure control. Upon clinical suspicion of a mitochondrial disease, WES was performed, followed by Sanger sequencing for confirmation of the findings.
OUTCOMES: The patient clinically improved, with cessation of seizures, recovery from pneumonia, and confirmed diagnosis of COXPD35.
LESSONS: The identification of new TRIT1 variants and the expanding phenotypic spectrum of COXPD35 provides insights into its clinical and genotypic characteristics. WES and Sanger Sequencing confirm the diagnosis of COXPD35; however, it can be challenging in resource-limited settings.

Keywords:  ; case report; combined oxidative phosphorylation deficiency 35 (COXPD35); mitochondrial disorder; whole-exome sequencing (WES)

DOI:  https://doi.org/10.1097/MD.0000000000047885
Trends Endocrinol Metab. 2026 Feb 24. pii: S1043-2760(26)00011-1. [Epub ahead of print]

Reversible phosphorylation influences energetic cellular metabolism by modulating mitochondrial gene expression.

Aldara Mainé-Rodrigo, Ana Vela-Sebastián, David Pacheu-Grau.

  Mitochondria act as key metabolic regulators beyond ATP production, and the understanding of how cellular signaling modifies mitochondrial gene expression is currently being explored. Recent evidence links kinases such as mitogen-activated protein kinase-interacting kinases, hexokinase 1, and eukaryotic elongation factor 2 kinase to mitochondrial function, influencing metabolic adaptation, inflammation, and survival under nutrient stress, with implications for obesity and aging.

Keywords:  cellular metabolism; mitochondria; mitochondrial gene expression; reversible phosphorylation

DOI:  https://doi.org/10.1016/j.tem.2026.01.011
Int J Mol Sci. 2026 Feb 07. pii: 1629. [Epub ahead of print]27(4):

G-Quadruplex Unwinding Molecular Mechanisms by Helicases and Their Applications.

Jiawen Sun, Yangzhi Wang, Yihua Huang, Zhongzhou Chen.

  G-quadruplexes (G4s) are specialized nucleic acid structures extensively formed throughout the genome, with particular enrichment in regulatory regions such as telomeres, promoters, and transcriptional enhancers. These four-stranded assemblies are involved in multiple chromosomal processes, including DNA replication, transcription, maintenance of genomic stability, and epigenetic regulation, and are closely associated with cancer biology. Due to their unusual thermodynamic stability, G4s serve as physical barriers to DNA/RNA unwinding, thereby impeding replication, transcription, and translation and compromising genome integrity. To mitigate this threat, cells have evolved dedicated helicases that can actively resolve G4 structures. In this review, we summarize recent structural advances-primarily derived from protein crystallography-regarding the mechanisms by which helicases unwind G4 quadruplexes. The insights presented herein establish a framework for elucidating the molecular basis of G4 unfolding and for the rational design of small-molecule G4 ligands and therapeutic agents. Additionally, we explore the applications of G4 helicases in nanopore sequencing, which aim to enhance sequencing accuracy, throughput, and continuity.

Keywords:  G-quadruplex; G4 ligand; drug design; helicase; nanopore sequencing; structural basis; telomere; unwinding

DOI:  https://doi.org/10.3390/ijms27041629