bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022‒10‒09
28 papers selected by
Catalina Vasilescu
University of Helsinki
  1. Two independent respiratory chains adapt OXPHOS performance to glycolytic switch.
  2. Inter-organellar and systemic responses to impaired mitochondrial matrix protein import in skeletal muscle.
  3. Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes.
  4. Pathogenic mtDNA variants, in particular single large-scale mtDNA deletions, are strongly associated with post-lingual onset sensorineural hearing loss in primary mitochondrial disease.
  5. Independent regulation of mitochondrial DNA quantity and quality in Caenorhabditis elegans primordial germ cells.
  6. Loss of Num1-mediated cortical dynein anchoring negatively impacts respiratory growth.
  7. A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome.
  8. Mechanisms and significance of tissue-specific MICU regulation of the mitochondrial calcium uniporter complex.
  9. Microfluidic devices as model platforms of CNS injury-ischemia to study axonal regeneration by regulating mitochondrial transport and bioenergetic metabolism.
  10. Cardiac Outcomes in Adults With Mitochondrial Diseases.
  11. Population-based, cross-sectional assessment of dietary patterns and supplement use in mitochondrial disease.
  12. Impediments to Heart Transplantation in Adults With MELASMT-TL1:m.3243A>G Cardiomyopathy.
  13. The Mitochondrial Unfolded Protein Response: A Novel Protective Pathway Targeting Cardiomyocytes.
  14. Miro1 regulates mitochondrial homeostasis and meiotic resumption of mouse oocyte.
  15. Mitochondrial fatty acid β-oxidation is important for normal osteoclast formation in growing female mice.
  16. Cell-Free Mitochondrial DNA in Acute Brain Injury.
  17. Movement disorders in valine métabolism diseases caused by HIBCH and ECHS1 deficiencies.
  18. Cognitive functioning and mental health in children with a primary mitochondrial disease.
  19. miR-181a/b downregulation: a mutation-independent therapeutic approach for inherited retinal diseases.
  20. Mitochondrial dynamics maintain muscle stem cell regenerative competence throughout adult life by regulating metabolism and mitophagy.
  21. Mitochondrial quality control proteases and their modulation for cancer therapy.
  22. Nuclear TCA cycle reactions.
  23. No role for nuclear transcription regulators in mammalian mitochondria?
  24. neuromaps: structural and functional interpretation of brain maps.
  25. Mesoscale structure-function relationships in mitochondrial transcriptional condensates.
  26. Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders.
  27. Hedgehog pathway is negatively regulated during the development of Drosophila melanogaster PheRS-m (Drosophila homologs gene of human FARS2) mutants.
  28. Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements.
  1. Cell Metab. 2022 Sep 28. pii: S1550-4131(22)00395-3. [Epub ahead of print]
    Two independent respiratory chains adapt OXPHOS performance to glycolytic switch.
    Erika Fernández-Vizarra, Sandra López-Calcerrada, Ana Sierra-Magro, Rafael Pérez-Pérez, Luke E Formosa, Daniella H Hock, María Illescas, Ana Peñas, Michele Brischigliaro, Shujing Ding, Ian M Fearnley, Charalampos Tzoulis, Robert D S Pitceathly, Joaquín Arenas, Miguel A Martín, David A Stroud, Massimo Zeviani, Michael T Ryan, Cristina Ugalde.
      The structural and functional organization of the mitochondrial respiratory chain (MRC) remains intensely debated. Here, we show the co-existence of two separate MRC organizations in human cells and postmitotic tissues, C-MRC and S-MRC, defined by the preferential expression of three COX7A subunit isoforms, COX7A1/2 and SCAFI (COX7A2L). COX7A isoforms promote the functional reorganization of distinct co-existing MRC structures to prevent metabolic exhaustion and MRC deficiency. Notably, prevalence of each MRC organization is reversibly regulated by the activation state of the pyruvate dehydrogenase complex (PDC). Under oxidative conditions, the C-MRC is bioenergetically more efficient, whereas the S-MRC preferentially maintains oxidative phosphorylation (OXPHOS) upon metabolic rewiring toward glycolysis. We show a link between the metabolic signatures converging at the PDC and the structural and functional organization of the MRC, challenging the widespread notion of the MRC as a single functional unit and concluding that its structural heterogeneity warrants optimal adaptation to metabolic function.
    Keywords:  COX7A1–2; SCAFI/COX7RP/COX7A2L; bioenergetics; glycolysis; metabolic switch; mitochondria; oxidative metabolism; pyruvate dehydrogenase; respiratory chain organizations; respiratory supercomplexes
    DOI:  https://doi.org/10.1016/j.cmet.2022.09.005
  2. Commun Biol. 2022 Oct 05. 5(1): 1060
    Inter-organellar and systemic responses to impaired mitochondrial matrix protein import in skeletal muscle.
    Nirajan Neupane, Jayasimman Rajendran, Jouni Kvist, Sandra Harjuhaahto, Bowen Hu, Veijo Kinnunen, Yang Yang, Anni I Nieminen, Henna Tyynismaa.
      Effective protein import from cytosol is critical for mitochondrial functions and metabolic regulation. We describe here the mammalian muscle-specific and systemic consequences to disrupted mitochondrial matrix protein import by targeted deletion of the mitochondrial HSP70 co-chaperone GRPEL1. Muscle-specific loss of GRPEL1 caused rapid muscle atrophy, accompanied by shut down of oxidative phosphorylation and mitochondrial fatty acid oxidation, and excessive triggering of proteotoxic stress responses. Transcriptome analysis identified new responders to mitochondrial protein import toxicity, such as the neurological disease-linked intermembrane space protein CHCHD10. Besides communication with ER and nucleus, we identified crosstalk of distressed mitochondria with peroxisomes, in particular the induction of peroxisomal Acyl-CoA oxidase 2 (ACOX2), which we propose as an ATF4-regulated peroxisomal marker of integrated stress response. Metabolic profiling indicated fatty acid enrichment in muscle, a shift in TCA cycle intermediates in serum and muscle, and dysregulated bile acids. Our results demonstrate the fundamental importance of GRPEL1 and provide a robust model for detecting mammalian inter-organellar and systemic responses to impaired mitochondrial matrix protein import and folding.
    DOI:  https://doi.org/10.1038/s42003-022-04034-z
  3. Nature. 2022 Oct 05.
    Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes.
    Wei Wei, Katherine R Schon, Greg Elgar, Andrea Orioli, Melanie Tanguy, Adam Giess, Marc Tischkowitz, Mark J Caulfield, Patrick F Chinnery.
      DNA transfer from cytoplasmic organelles to the cell nucleus is a legacy of the endosymbiotic event-the majority of nuclear-mitochondrial segments (NUMTs) are thought to be ancient, preceding human speciation1-3. Here we analyse whole-genome sequences from 66,083 people-including 12,509 people with cancer-and demonstrate the ongoing transfer of mitochondrial DNA into the nucleus, contributing to a complex NUMT landscape. More than 99% of individuals had at least one of 1,637 different NUMTs, with 1 in 8 individuals having an ultra-rare NUMT that is present in less than 0.1% of the population. More than 90% of the extant NUMTs that we evaluated inserted into the nuclear genome after humans diverged from apes. Once embedded, the sequences were no longer under the evolutionary constraint seen within the mitochondrion, and NUMT-specific mutations had a different mutational signature to mitochondrial DNA. De novo NUMTs were observed in the germline once in every 104 births and once in every 103 cancers. NUMTs preferentially involved non-coding mitochondrial DNA, linking transcription and replication to their origin, with nuclear insertion involving multiple mechanisms including double-strand break repair associated with PR domain zinc-finger protein 9 (PRDM9) binding. The frequency of tumour-specific NUMTs differed between cancers, including a probably causal insertion in a myxoid liposarcoma. We found evidence of selection against NUMTs on the basis of size and genomic location, shaping a highly heterogenous and dynamic human NUMT landscape.
    DOI:  https://doi.org/10.1038/s41586-022-05288-7
  4. Mol Genet Metab. 2022 Sep 19. pii: S1096-7192(22)00398-5. [Epub ahead of print]137(3): 230-238
    Pathogenic mtDNA variants, in particular single large-scale mtDNA deletions, are strongly associated with post-lingual onset sensorineural hearing loss in primary mitochondrial disease.
    Johanna Elander, Elizabeth M McCormick, Maria Värendh, Karin Stenfeldt, Rebecca D Ganetzky, Amy Goldstein, Zarazuela Zolkipli-Cunningham, Laura E MacMullen, Rui Xiao, Marni J Falk, Johannes K Ehinger.
      In this retrospective cohort study of 193 consecutive subjects with primary mitochondrial disease (PMD) seen at the Children's Hospital of Philadelphia Mitochondrial Medicine Frontier Program, we assessed prevalence, severity, and time of onset of sensorineural hearing loss (SNHL) for PMD cases with different genetic etiologies. Subjects were grouped by genetic diagnosis: mitochondrial DNA (mtDNA) pathogenic variants, single large-scale mtDNA deletions (SLSMD), or nuclear DNA (nDNA) pathogenic variants. SNHL was audiometrically confirmed in 27% of PMD subjects (20% in mtDNA pathogenic variants, 58% in SLSMD and 25% in nDNA pathogenic variants). SLSMD had the highest odds ratio for SNHL. SNHL onset was post-lingual in 79% of PMD cases, interestingly including all cases with mtDNA pathogenic variants and SLSMD, which was significantly different from PMD cases caused by nDNA pathogenic variants. SNHL onset during school age was predominant in this patient population. Regular audiologic assessment is important for PMD patients, and PMD of mtDNA etiology should be considered as a differential diagnosis in pediatric patients and young adults with post-lingual SNHL onset, particularly in the setting of multi-system clinical involvement. Pathogenic mtDNA variants and SLSMD are less likely etiologies in subjects with congenital, pre-lingual onset SNHL.
    Keywords:  Audiology; Mitochondria; Mitochondrial DNA; Mitochondrial disease; Primary mitochondrial disease; Sensorineural hearing loss
    DOI:  https://doi.org/10.1016/j.ymgme.2022.09.002
  5. Elife. 2022 Oct 06. pii: e80396. [Epub ahead of print]11
    Independent regulation of mitochondrial DNA quantity and quality in Caenorhabditis elegans primordial germ cells.
    Aaron Z A Schwartz, Nikita Tsyba, Yusuff Abdu, Maulik R Patel, Jeremy Nance.
      Mitochondria harbor an independent genome, called mitochondrial DNA (mtDNA), which contains essential metabolic genes. Although mtDNA mutations occur at high frequency, they are inherited infrequently, indicating that germline mechanisms limit their accumulation. To determine how germline mtDNA is regulated, we examined the control of mtDNA quantity and quality in C. elegans primordial germ cells (PGCs). We show that PGCs combine strategies to generate a low point in mtDNA number by segregating mitochondria into lobe-like protrusions that are cannibalized by adjacent cells, and by concurrently eliminating mitochondria through autophagy, reducing overall mtDNA content twofold. As PGCs exit quiescence and divide, mtDNAs replicate to maintain a set point of ~200 mtDNAs per germline stem cell. Whereas cannibalism and autophagy eliminate mtDNAs stochastically, we show that the kinase PTEN-induced kinase 1 (PINK1), operating independently of Parkin and autophagy, preferentially reduces the fraction of mutant mtDNAs. Thus, PGCs employ parallel mechanisms to control both the quantity and quality of the founding population of germline mtDNAs.
    Keywords:  C. elegans; PINK1; autophagy; bottleneck; cell biology; developmental biology; mitochondrial DNA; primordial germ cells; purifying selection
    DOI:  https://doi.org/10.7554/eLife.80396
  6. J Cell Sci. 2022 Oct 03. pii: jcs.259980. [Epub ahead of print]
    Loss of Num1-mediated cortical dynein anchoring negatively impacts respiratory growth.
    Antoineen J White, Clare S Harper, Erica M Rosario, Jonathan V Dietz, Hannah G Addis, Jennifer L Fox, Oleh Khalimonchuk, Laura L Lackner.
      Num1 is a multifunctional protein that both tethers mitochondria to the plasma membrane and anchors dynein to the cell cortex during nuclear inheritance. Previous work has examined the impact loss of Num1-based mitochondrial tethering has on dynein function in Saccharomyces cerevisiae; here, we elucidate its impact on mitochondrial function. We find that like mitochondria, Num1 is regulated by changes in metabolic state, with the protein levels and cortical distribution of Num1 differing between fermentative and respiratory growth conditions. In cells lacking Num1, we observe a reproducible respiratory growth defect, suggesting a role for Num1 in not only maintaining mitochondrial morphology, but also function. A structure-function approach revealed that, unexpectedly, Num1-mediated cortical dynein anchoring is important for normal growth under respiratory conditions. The severe respiratory growth defect in Δnum1 cells is not specifically due to dynein's canonical function in nuclear migration but is dependent on the presence of dynein, as deletion of DYN1 in Δnum1 cells partially rescues respiratory growth. We hypothesize that misregulated dynein present in cells that lack Num1 negatively impacts mitochondrial function resulting in defects in respiratory growth.
    Keywords:  membrane contact sites; mitochondria; organelle positioning
    DOI:  https://doi.org/10.1242/jcs.259980
  7. Nat Commun. 2022 Oct 06. 13(1): 5902
    A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome.
    Ieva Keraite, Philipp Becker, Davide Canevazzi, Cristina Frias-López, Marc Dabad, Raúl Tonda-Hernandez, Ida Paramonov, Matthew John Ingham, Isabelle Brun-Heath, Jordi Leno, Anna Abulí, Elena Garcia-Arumí, Simon Charles Heath, Marta Gut, Ivo Glynne Gut.
      Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research.
    DOI:  https://doi.org/10.1038/s41467-022-33530-3
  8. Mol Cell. 2022 Oct 06. pii: S1097-2765(22)00895-4. [Epub ahead of print]82(19): 3661-3676.e8
    Mechanisms and significance of tissue-specific MICU regulation of the mitochondrial calcium uniporter complex.
    Chen-Wei Tsai, Madison X Rodriguez, Anna M Van Keuren, Charles B Phillips, Hannah M Shushunov, Jessica E Lee, Anastacia M Garcia, Amrut V Ambardekar, Joseph C Cleveland, Julie A Reisz, Catherine Proenza, Kathryn C Chatfield, Ming-Feng Tsai.
      Mitochondrial Ca2+ uptake, mediated by the mitochondrial Ca2+ uniporter, regulates oxidative phosphorylation, apoptosis, and intracellular Ca2+ signaling. Previous studies suggest that non-neuronal uniporters are exclusively regulated by a MICU1-MICU2 heterodimer. Here, we show that skeletal-muscle and kidney uniporters also complex with a MICU1-MICU1 homodimer and that human/mouse cardiac uniporters are largely devoid of MICUs. Cells employ protein-importation machineries to fine-tune the relative abundance of MICU1 homo- and heterodimers and utilize a conserved MICU intersubunit disulfide to protect properly assembled dimers from proteolysis by YME1L1. Using the MICU1 homodimer or removing MICU1 allows mitochondria to more readily take up Ca2+ so that cells can produce more ATP in response to intracellular Ca2+ transients. However, the trade-off is elevated ROS, impaired basal metabolism, and higher susceptibility to death. These results provide mechanistic insights into how tissues can manipulate mitochondrial Ca2+ uptake properties to support their unique physiological functions.
    Keywords:  calcium channels; cardiac pathophysiology; cellular metabolism; intracellular calcium signaling; membrane-transport mechanisms; mitochondrial physiology; mitochondrial proteases; organellar channels; protein complexes
    DOI:  https://doi.org/10.1016/j.molcel.2022.09.006
  9. Cell Regen. 2022 Oct 03. 11(1): 33
    Microfluidic devices as model platforms of CNS injury-ischemia to study axonal regeneration by regulating mitochondrial transport and bioenergetic metabolism.
    Ning Huang, Zu-Hang Sheng.
      Central nervous system (CNS) neurons typically fail to regenerate their axons after injury leading to neurological impairment. Axonal regeneration is a highly energy-demanding cellular program that requires local mitochondria to supply most energy within injured axons. Recent emerging lines of evidence have started to reveal that injury-triggered acute mitochondrial damage and local energy crisis contribute to the intrinsic energetic restriction that accounts for axon regeneration failure in the CNS. Characterizing and reprogramming bioenergetic signaling and mitochondrial maintenance after axon injury-ischemia is fundamental for developing therapeutic strategies that can restore local energy metabolism and thus facilitate axon regeneration. Therefore, establishing reliable and reproducible neuronal model platforms is critical for assessing axonal energetic metabolism and regeneration capacity after injury-ischemia. In this focused methodology article, we discuss recent advances in applying cutting-edge microfluidic chamber devices in combination with state-of-the-art live-neuron imaging tools to monitor axonal regeneration, mitochondrial transport, bioenergetic metabolism, and local protein synthesis in response to injury-ischemic stress in mature CNS neurons.
    Keywords:  Axon injury; Axon regeneration; Axonal bioenergetics; Axonal protein synthesis; Ischemia; Microfluidic device; Mitochondrial transport
    DOI:  https://doi.org/10.1186/s13619-022-00138-3
  10. J Am Coll Cardiol. 2022 Oct 11. pii: S0735-1097(22)06527-5. [Epub ahead of print]80(15): 1421-1430
    Cardiac Outcomes in Adults With Mitochondrial Diseases.
    Konstantinos Savvatis, Christoffer Rasmus Vissing, Lori Klouvi, Anca Florian, Mehjabin Rahman, Anthony Béhin, Abdallah Fayssoil, Marion Masingue, Tanya Stojkovic, Henri Marc Bécane, Nawal Berber, Fanny Mochel, Denis Duboc, Bertrand Fontaine, Bjørg Krett, Caroline Stalens, Julie Lejeune, Robert D S Pitceathly, Luis Lopes, Malika Saadi, Thomas Gossios, Vincent Procaccio, Marco Spinazzi, Céline Tard, Pascal De Groote, Claire-Marie Dhaenens, Claire Douillard, Andoni Echaniz-Laguna, Ros Quinlivan, Michael G Hanna, Ali Yilmaz, John Vissing, Pascal Laforêt, Perry Elliott, Karim Wahbi.
      BACKGROUND: Patients with mitochondrial diseases are at risk of heart failure (HF) and arrhythmic major adverse cardiac events (MACE).OBJECTIVES: We developed prediction models to estimate the risk of HF and arrhythmic MACE in this population.
    METHODS: We determined the incidence and searched for predictors of HF and arrhythmic MACE using Cox regression in 600 adult patients from a multicenter registry with genetically confirmed mitochondrial diseases.
    RESULTS: Over a median follow-up time of 6.67 years, 29 patients (4.9%) reached the HF endpoint, including 19 hospitalizations for nonterminal HF, 2 cardiac transplantations, and 8 deaths from HF. Thirty others (5.1%) reached the arrhythmic MACE, including 21 with third-degree or type II second-degree atrioventricular blocks, 4 with sinus node dysfunction, and 5 sudden cardiac deaths. Predictors of HF were the m.3243A>G variant (HR: 4.3; 95% CI: 1.8-10.1), conduction defects (HR: 3.0; 95% CI: 1.3-6.9), left ventricular (LV) hypertrophy (HR: 2.6; 95% CI: 1.1-5.8), LV ejection fraction <50% (HR: 10.2; 95% CI: 4.6-22.3), and premature ventricular beats (HR: 4.1; 95% CI: 1.7-9.9). Independent predictors for arrhythmia were single, large-scale mtDNA deletions (HR: 4.3; 95% CI: 1.7-10.4), conduction defects (HR: 6.8; 95% CI: 3.0-15.4), and LV ejection fraction <50% (HR: 2.7; 95% CI: 1.1-7.1). C-indexes of the Cox regression models were 0.91 (95% CI: 0.88-0.95) and 0.80 (95% CI: 0.70-0.90) for the HF and arrhythmic MACE, respectively.
    CONCLUSIONS: We developed the first prediction models for HF and arrhythmic MACE in patients with mitochondrial diseases using genetic variant type and simple cardiac assessments.
    Keywords:  conduction disease; heart failure; m3243A>G; mitochondrial diseases; single large-scale deletions; sudden death
    DOI:  https://doi.org/10.1016/j.jacc.2022.08.716
  11. Clin Nutr ESPEN. 2022 Oct;pii: S2405-4577(22)00310-2. [Epub ahead of print]51 461-469
    Population-based, cross-sectional assessment of dietary patterns and supplement use in mitochondrial disease.
    Robyn F Madden, Sophie Lalonde-Bester, Jill A Parnell, Melanie S Trudeau, Julia M Martin, Aneal Khan, Jane Shearer.
      BACKGROUND & AIMS: Mitochondrial diseases (MITO) are a large group of rare genetic conditions that manifest in high-energy organ systems and impair mitochondrial oxidative phosphorylation. Therapeutic management often involves the use of dietary supplements and special dietary patterns.METHODS: A questionnaire assessing dietary patterns and supplement use was administered to diagnosed patients or their surrogate caregivers through various MITO-related patient and advocacy organizations and social media internationally from March to September 2021. Secondary outcomes assessed information available to participants regarding supplements, and factors influencing use, knowledge, and adherence to dietary supplements. Supplements were classified using standard criteria. A total of 236 responses were used for the analysis.
    RESULTS: The average number of supplements taken among patients was 7.0 (±5.0 SD) with over 70% reporting taking more than 4 supplements. Sixty percent of respondents reported dietary restrictions, while 14% were tube fed or parenterally fed. Uncertainty regarding supplement cost, use, and availability were a significant source of stress for most participants with 61% of patients reporting no financial coverage for supplementation and 45% reporting no coverage for special dietary needs.
    CONCLUSIONS: Adequate scientific evidence for the widespread use of dietary supplements in MITO is lacking. As a result, there is excessive supplementation in MITO that imposes significant stress on patients. Future studies are needed to evaluate the efficacy of specific supplements as well as special dietary patterns to enable physicians and pharmacists to provide evidence-based recommendations to patients to reduce symptoms, as well as the emotional and financial strain associated with supplement use.
    Keywords:  Dietary supplements; Mitochondrial disease; Nutrition; Rare disease; Survey
    DOI:  https://doi.org/10.1016/j.clnesp.2022.06.016
  12. J Am Coll Cardiol. 2022 Oct 11. pii: S0735-1097(22)06530-5. [Epub ahead of print]80(15): 1431-1443
    Impediments to Heart Transplantation in Adults With MELASMT-TL1:m.3243A>G Cardiomyopathy.
    Alessandro Di Toro, Mario Urtis, Nupoor Narula, Lorenzo Giuliani, Maurizia Grasso, Michele Pasotti, Carlo Pellegrini, Alessandra Serio, Andrea Pilotto, Elena Antoniazzi, Teresa Rampino, Lorenzo Magrassi, Adele Valentini, Anna Cavallini, Laura Scelsi, Stefano Ghio, Massimo Abelli, Iacopo Olivotto, Maurizio Porcu, Antonello Gavazzi, Takahide Kodama, Eloisa Arbustini.
      BACKGROUND: The heart is commonly involved in maternally inherited mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome caused by the MT-TL1 m.3243A>G mutation of the mitochondrial DNA. Heart transplantation (HTx) is controversial and has rarely been performed with conflicting results.OBJECTIVES: We analyzed factors preventing HTx in consecutive adult patients with MELASMT-TL1:m.3243A>G cardiomyopathy diagnosed and followed during the last 23 years in our HTx referral center.
    METHODS: The series consists of 14 unrelated adult probands who were referred for evaluation of cardiomyopathy from 1998 to 2021. None had a suspected diagnosis of MELAS before referral. All patients underwent clinical and genetic visit and counseling, mitochondrial DNA sequencing, cardiovascular investigation (including right heart catheterization and endomyocardial biopsy in 10), multidisciplinary assessment, and biochemical tests. Family screening identified 2 affected relatives.
    RESULTS: The cardiac phenotype was characterized by hypertrophic, concentric, nonobstructive cardiomyopathy that often evolved into a dilated cardiomyopathy-like phenotype. Of the 14 probands, 7 were potential candidates for HTx, 2 for heart and kidney Tx, and 1 was on the active HTx list for 3 years. None of the 10 probands underwent HTx. One is currently being evaluated for HTx. All had diabetes, hearing loss, and myopathy, and 10 had chronic kidney disease and progressive encephalomyopathy. During follow-up, 10 died from heart failure associated with multiorgan failure within 5 years of the genetic diagnosis.
    CONCLUSIONS: High risk of stroke-like episodes, chronic kidney disease, and wasting myopathy in MELASMT-TL1:m.3243A>G patients prevents activation of plans for HTx. As a result, the management of their cardiomyopathy in this syndromic context remains an unmet clinical need.
    Keywords:  MELAS; MT-TL1:m.3243A>G; heart transplantation; mitochondrial cardiomyopathy
    DOI:  https://doi.org/10.1016/j.jacc.2022.04.067
  13. Oxid Med Cell Longev. 2022 ;2022 6430342
    The Mitochondrial Unfolded Protein Response: A Novel Protective Pathway Targeting Cardiomyocytes.
    Jinfeng Liu, Xinyong He, Sicheng Zheng, Aisong Zhu, Junyan Wang.
      Mitochondrial protein homeostasis in cardiomyocyte injury determines not only the normal operation of mitochondrial function but also the fate of mitochondria in cardiomyocytes. Studies of mitochondrial protein homeostasis have become an integral part of cardiovascular disease research. Modulation of the mitochondrial unfolded protein response (UPRmt), a protective factor for cardiomyocyte mitochondria, may in the future become an important treatment strategy for myocardial protection in cardiovascular disease. However, because of insufficient understanding of the UPRmt and inadequate elucidation of relevant mechanisms, few therapeutic drugs targeting the UPRmt have been developed. The UPRmt maintains a series of chaperone proteins and proteases and is activated when misfolded proteins accumulate in the mitochondria. Mitochondrial injury leads to metabolic dysfunction in cardiomyocytes. This paper reviews the relationship of the UPRmt and mitochondrial quality monitoring with cardiomyocyte protection. This review mainly introduces the regulatory mechanisms of the UPRmt elucidated in recent years and the relationship between the UPRmt and mitophagy, mitochondrial fusion/fission, mitochondrial biosynthesis, and mitochondrial energy metabolism homeostasis in order to generate new ideas for the study of the mitochondrial protein homeostasis mechanisms as well as to provide a reference for the targeted drug treatment of imbalances in mitochondrial protein homeostasis following cardiomyocyte injury.
    DOI:  https://doi.org/10.1155/2022/6430342
  14. J Cell Physiol. 2022 Oct 02.
    Miro1 regulates mitochondrial homeostasis and meiotic resumption of mouse oocyte.
    Yue Xue, Tie-Gang Meng, Ying-Chun Ouyang, Sai-Li Liu, Jia-Ni Guo, Zhen-Bo Wang, Heide Schatten, Chun-Ying Song, Xing-Ping Guo, Qing-Yuan Sun.
      Miro1, a mitochondrial Rho GTPase1, is a kind of mitochondrial outer membrane protein involved in the regulation of mitochondrial anterograde transport and its subcellular distribution. Mitochondria influence reproductive processes of mammals in some aspects. Mitochondria are important for oocyte maturation, fertilization and embryonic development. The purpose of this study was to evaluate whether Miro1 regulates mouse oocyte maturation by altering mitochondrial homeostasis. We showed that Miro1 was expressed in mouse oocyte at different maturation stages. Miro1 mainly distributed in the cytoplasm and around the spindle during oocyte maturation. Small interference RNA-mediated Miro1 depletion caused significantly abnormal distribution of mitochondria and endoplasmic reticulum as well as mitochondrial dysfunction, resulting in severely impaired germinal vesicle breakdown (GVBD) of mouse oocytes. For those oocytes which went through GVBD in the Miro1-depleted group, part of them were inhibited in meiotic prophase I stage with abnormal chromosome arrangement and scattered spindle length. Our results suggest that Miro1 is essential for maintaining the maturation potential of mouse oocyte.
    Keywords:  Miro1; Mitochondria; meiosis; oocyte
    DOI:  https://doi.org/10.1002/jcp.30890
  15. Front Physiol. 2022 ;13 997358
    Mitochondrial fatty acid β-oxidation is important for normal osteoclast formation in growing female mice.
    Priyanka Kushwaha, Nathalie S Alekos, Soohyun P Kim, Zhu Li, Michael J Wolfgang, Ryan C Riddle.
      Skeletal remodeling is an energy demanding process that is linked to nutrient availability and the levels of metabolic hormones. While recent studies have examined the metabolic requirements of bone formation by osteoblasts, much less is known about the energetic requirements of bone resorption by osteoclasts. The abundance of mitochondria in mature osteoclasts suggests that the production of an acidified micro-environment conducive to the ionization of hydroxyapatite, secretion of matrix-degrading enzymes, and motility during resorption requires significant energetic capacity. To investigate the contribution of mitochondrial long chain fatty acid β-oxidation to osteoclast development, we disrupted the expression of carnitine palmitoyltransferase-2 (Cpt2) in myeloid-lineage cells. Fatty acid oxidation increases dramatically in bone marrow cultures stimulated with RANKL and M-CSF and microCT analysis revealed that the genetic inhibition of long chain fatty acid oxidation in osteoclasts significantly increases trabecular bone volume in female mice secondary to reduced osteoclast numbers. In line with these data, osteoclast precursors isolated from Cpt2 mutants exhibit reduced capacity to form large-multinucleated osteoclasts, which was not rescued by exogenous glucose or pyruvate, and signs of an energetic stress response. Together, our data demonstrate that mitochondrial long chain fatty acid oxidation by the osteoclast is required for normal bone resorption as its inhibition produces an intrinsic defect in osteoclast formation.
    Keywords:  CPT2; bone; glucose; lipid metabolism; osteoclast
    DOI:  https://doi.org/10.3389/fphys.2022.997358
  16. Neurotrauma Rep. 2022 ;3(1): 415-420
    Cell-Free Mitochondrial DNA in Acute Brain Injury.
    Saeed Kayhanian, Angelos Glynos, Richard Mair, Andras Lakatos, Peter J A Hutchinson, Adel E Helmy, Patrick F Chinnery.
      Traumatic brain injury and aneurysmal subarachnoid haemorrhage are a major cause of morbidity and mortality worldwide. Treatment options remain limited and are hampered by our understanding of the cellular and molecular mechanisms, including the inflammatory response observed in the brain. Mitochondrial DNA (mtDNA) has been shown to activate an innate inflammatory response by acting as a damage-associated molecular pattern (DAMP). Here, we show raised circulating cell-free (ccf) mtDNA levels in both cerebrospinal fluid (CSF) and serum within 48 h of brain injury. CSF ccf-mtDNA levels correlated with clinical severity and the interleukin-6 cytokine response. These findings support the use of ccf-mtDNA as a biomarker after acute brain injury linked to the inflammatory disease mechanism.
    Keywords:  DAMP; acute brain injury; brain inflammation; mitochondrial DNA; subarachnoid hemorrhage; traumatic brain injury
    DOI:  https://doi.org/10.1089/neur.2022.0032
  17. Eur J Neurol. 2022 Nov;29(11): 3229-3242
    Movement disorders in valine métabolism diseases caused by HIBCH and ECHS1 deficiencies.
    Marie-Céline François-Heude, Elise Lebigot, Emmanuel Roze, Marie Thérèse Abi Warde, Claude Cances, Lena Damaj, Caroline Espil, Joel Fluss, Pascale de Lonlay, Ilse Kern, Guy Lenaers, Arnold Munnich, Pierre Meyer, Marie-Aude Spitz, Stéphanie Torre, Diane Doummar, Guy Touati, Nicolas Leboucq, Agathe Roubertie.
      BACKGROUND AND PURPOSE: HIBCH and ECHS1 genes encode two enzymes implicated in the critical steps of valine catabolism, 3-hydroxyisobutyryl-coenzyme A (CoA) hydrolase (HIBCH) and short-chainenoyl-CoA hydratase (ECHS1), respectively. HIBCH deficiency (HIBCHD) and ECHS1 deficiency (ECHS1D) generate rare metabolic dysfunctions, often revealed by neurological symptoms. The aim of this study was to describe movement disorders spectrum in patients with pathogenic variants in ECHS1 and HIBC.METHODS: We reviewed a series of 18 patients (HIBCHD: 5; ECHS1D: 13) as well as 105 patients from the literature. We analysed the detailed phenotype of HIBCHD (38 patients) and ECHS1D (85 patients), focusing on MDs.
    RESULTS: The two diseases have a very similar neurological phenotype, with an early onset before 10 years of age for three clinical presentations: neonatal onset, Leigh-like syndrome (progressive onset or acute neurological decompensation), and isolated paroxysmal dyskinesia. Permanent or paroxysmal MDs were recorded in 61% of HIBCHD patients and 72% of ECHS1D patients. Patients had a variable combination of either isolated or combined MD, and dystonia was the main MD. These continuous MDs included dystonia, chorea, parkinsonism, athetosis, myoclonus, tremors, and abnormal eye movements. Patients with paroxysmal dyskinesia (HIBCHD: 4; ECHS1D: 9) usually had pure paroxysmal dystonia with normal clinical examination and no major impairment in psychomotor development. No correlation could be identified between clinical pattern (especially MD) and genetic pathogenic variants.
    CONCLUSIONS: Movement disorders, including abnormal ocular movements, are a hallmark of HIBCHD and ECHS1D. MDs are not uniform; dystonia is the most frequent, and various types of MD are combined in single patient.
    Keywords:  ECHS1; HIBCH; dystonia; inherited metabolic disease
    DOI:  https://doi.org/10.1111/ene.15515
  18. Orphanet J Rare Dis. 2022 Oct 01. 17(1): 368
    Cognitive functioning and mental health in children with a primary mitochondrial disease.
    Kim F E van de Loo, José A E Custers, Lonneke de Boer, Marloes van Lieshout, Maaike C de Vries, Mirian C H Janssen, Christianne M Verhaak.
      BACKGROUND: Studies regarding cognitive and mental health functioning in children with mitochondrial disease (MD) are scarce, while both are important issues given their impact on QoL. Knowledge on these aspects of functioning and its relationship with disease parameters is essential to gather more insight in working mechanisms and provide recommendations for future research and patientcare. The aim of this study was to map the cognitive functioning and mental health in children with MD in relation to disease specific factors.METHODS: Pediatric patients (< 18 year) with a genetically confirmed MD were included. Demographic and disease specific factors (International Paediatric Mitochondrial Disease Scale) were assessed, as well as cognitive functioning (intelligence, attention, working memory (WM)), and mental health (psychological functioning and quality of life). Individual patient data was described.
    RESULTS: Thirty-three children with MD were included. Intellectual functioning ranged from a clinically low IQ (36% of the patients, N = 12/33) to an average or above average IQ (39%, N = 13/33). A higher verbal versus performance IQ was observed (36% N = 5/14), a lower processing speed (43%, N = 6/14), attentional problems (50%, N = 7/14), and verbal WM problems (11%, N = 2/18). Regarding mental health, general behavioral problems were reported (45%, N = 10/22), and on subscale level, attention problems (45%, N = 10), withdrawn/depressed (36%, N = 8/22) and anxious/depressed behavior (14%, N = 3/22). Furthermore, QoL impairments were reported (42%, N = 5/12). The specific intelligence profiles, cognitive impairments, behavioral problems and QoL impairments occurred in every intelligence subgroup. Children with an average or above general intellectual functioning had a generally lower and less variability in IPMDS scores, less frequently epilepsy, vision and hearing problems, and a relatively later age of onset, as compared to patients with a clinically low intellectual functioning.
    CONCLUSIONS: Despite considerable heterogeneity, overall results showed a high rate of impairments in both cognitive and mental health functioning. Also in children with an average or above level of intellectual functioning, specific cognitive impairments were observed. Children with a clinically low intellectual functioning more often had disease related impairments compared to children with a higher intellectual functioning. The importance of structural assessment of cognitive functioning and mental health is warranted, also in children with mild disease related symptoms.
    Keywords:  Attention; Cognitive functioning; Disease manifestation; Mental health; Mitochondrial disease; Quality of life; Working memory
    DOI:  https://doi.org/10.1186/s13023-022-02510-7
  19. EMBO Mol Med. 2022 Oct 04. e15941
    miR-181a/b downregulation: a mutation-independent therapeutic approach for inherited retinal diseases.
    Sabrina Carrella, Martina Di Guida, Simona Brillante, Davide Piccolo, Ludovica Ciampi, Irene Guadagnino, Jorge Garcia Piqueras, Mariateresa Pizzo, Elena Marrocco, Marta Molinari, Georgios Petrogiannakis, Sara Barbato, Yulia Ezhova, Alberto Auricchio, Brunella Franco, Elvira De Leonibus, Enrico Maria Surace, Alessia Indrieri, Sandro Banfi.
      Inherited retinal diseases (IRDs) are a group of diseases whose common landmark is progressive photoreceptor loss. The development of gene-specific therapies for IRDs is hampered by their wide genetic heterogeneity. Mitochondrial dysfunction is proving to constitute one of the key pathogenic events in IRDs; hence, approaches that enhance mitochondrial activities have a promising therapeutic potential for these conditions. We previously reported that miR-181a/b downregulation boosts mitochondrial turnover in models of primary retinal mitochondrial diseases. Here, we show that miR-181a/b silencing has a beneficial effect also in IRDs. In particular, the injection in the subretinal space of an adeno-associated viral vector (AAV) that harbors a miR-181a/b inhibitor (sponge) sequence (AAV2/8-GFP-Sponge-miR-181a/b) improves retinal morphology and visual function both in models of autosomal dominant (RHO-P347S) and of autosomal recessive (rd10) retinitis pigmentosa. Moreover, we demonstrate that miR-181a/b downregulation modulates the level of the mitochondrial fission-related protein Drp1 and rescues the mitochondrial fragmentation in RHO-P347S photoreceptors. Overall, these data support the potential use of miR-181a/b downregulation as an innovative mutation-independent therapeutic strategy for IRDs, which can be effective both to delay disease progression and to aid gene-specific therapeutic approaches.
    Keywords:  inherited retinal diseases; miR-181; mitochondria; photoreceptor; therapy
    DOI:  https://doi.org/10.15252/emmm.202215941
  20. Cell Stem Cell. 2022 Oct 06. pii: S1934-5909(22)00379-4. [Epub ahead of print]29(10): 1506-1508
    Mitochondrial dynamics maintain muscle stem cell regenerative competence throughout adult life by regulating metabolism and mitophagy.
    Xiaotong Hong, Joan Isern, Silvia Campanario, Eusebio Perdiguero, Ignacio Ramírez-Pardo, Jessica Segalés, Pablo Hernansanz-Agustín, Andrea Curtabbi, Oleg Deryagin, Angela Pollán, José A González-Reyes, José M Villalba, Marco Sandri, Antonio L Serrano, José A Enríquez, Pura Muñoz-Cánoves.
      
    DOI:  https://doi.org/10.1016/j.stem.2022.09.002
  21. Med Res Rev. 2022 Oct 08.
    Mitochondrial quality control proteases and their modulation for cancer therapy.
    Jiangnan Zhang, Wenliang Qiao, Youfu Luo.
      Mitochondria, the main provider of energy in eukaryotic cells, contains more than 1000 different proteins and is closely related to the development of cells. However, damaged proteins impair mitochondrial function, further contributing to several human diseases. Evidence shows mitochondrial proteases are critically important for protein maintenance. Most importantly, quality control enzymes exert a crucial role in the modulation of mitochondrial functions by degrading misfolded, aged, or superfluous proteins. Interestingly, cancer cells thrive under stress conditions that damage proteins, so targeting mitochondrial quality control proteases serves as a novel regulator for cancer cells. Not only that, mitochondrial quality control proteases have been shown to affect mitochondrial dynamics by regulating the morphology of optic atrophy 1 (OPA1), which is closely related to the occurrence and progression of cancer. In this review, we introduce mitochondrial quality control proteases as promising targets and related modulators in cancer therapy with a focus on caseinolytic protease P (ClpP), Lon protease (LonP1), high-temperature requirement protein A2 (HrtA2), and OMA-1. Further, we summarize our current knowledge of the advances in clinical trials for modulators of mitochondrial quality control proteases. Overall, the content proposed above serves to suggest directions for the development of novel antitumor drugs.
    Keywords:  activator; cancer therapy; inhibitor; mitochondrial proteases; quality control
    DOI:  https://doi.org/10.1002/med.21929
  22. Nat Cell Biol. 2022 Oct 06.
    Nuclear TCA cycle reactions.
    Melina Casadio.
      
    DOI:  https://doi.org/10.1038/s41556-022-01006-7
  23. Mol Cell. 2022 Sep 20. pii: S1097-2765(22)00899-1. [Epub ahead of print]
    No role for nuclear transcription regulators in mammalian mitochondria?
    Diana Rubalcava-Gracia, Rodolfo García-Villegas, Nils-Göran Larsson.
      Although the mammalian mtDNA transcription machinery is simple and resembles bacteriophage systems, there are many reports that nuclear transcription regulators, as exemplified by MEF2D, MOF, PGC-1α, and hormone receptors, are imported into mammalian mitochondria and directly interact with the mtDNA transcription machinery. However, the supporting experimental evidence for this concept is open to alternate interpretations, and a main issue is the difficulty in distinguishing indirect regulation of mtDNA transcription, caused by altered nuclear gene expression, from direct intramitochondrial effects. We provide a critical discussion and experimental guidelines to stringently assess roles of intramitochondrial factors implicated in direct regulation of mammalian mtDNA transcription.
    DOI:  https://doi.org/10.1016/j.molcel.2022.09.010
  24. Nat Methods. 2022 Oct 06.
    neuromaps: structural and functional interpretation of brain maps.
    Ross D Markello, Justine Y Hansen, Zhen-Qi Liu, Vincent Bazinet, Golia Shafiei, Laura E Suárez, Nadia Blostein, Jakob Seidlitz, Sylvain Baillet, Theodore D Satterthwaite, M Mallar Chakravarty, Armin Raznahan, Bratislav Misic.
      Imaging technologies are increasingly used to generate high-resolution reference maps of brain structure and function. Comparing experimentally generated maps to these reference maps facilitates cross-disciplinary scientific discovery. Although recent data sharing initiatives increase the accessibility of brain maps, data are often shared in disparate coordinate systems, precluding systematic and accurate comparisons. Here we introduce neuromaps, a toolbox for accessing, transforming and analyzing structural and functional brain annotations. We implement functionalities for generating high-quality transformations between four standard coordinate systems. The toolbox includes curated reference maps and biological ontologies of the human brain, such as molecular, microstructural, electrophysiological, developmental and functional ontologies. Robust quantitative assessment of map-to-map similarity is enabled via a suite of spatial autocorrelation-preserving null models. neuromaps combines open-access data with transparent functionality for standardizing and comparing brain maps, providing a systematic workflow for comprehensive structural and functional annotation enrichment analysis of the human brain.
    DOI:  https://doi.org/10.1038/s41592-022-01625-w
  25. Proc Natl Acad Sci U S A. 2022 Oct 11. 119(41): e2207303119
    Mesoscale structure-function relationships in mitochondrial transcriptional condensates.
    Marina Feric, Azadeh Sarfallah, Furqan Dar, Dmitry Temiakov, Rohit V Pappu, Tom Misteli.
      In live cells, phase separation is thought to organize macromolecules into membraneless structures known as biomolecular condensates. Here, we reconstituted transcription in condensates from purified mitochondrial components using optimized in vitro reaction conditions to probe the structure-function relationships of biomolecular condensates. We find that the core components of the mt-transcription machinery form multiphasic, viscoelastic condensates in vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than in solution. The condensate-mediated decrease in transcriptional rates is associated with the formation of vesicle-like structures that are driven by the production and accumulation of RNA during transcription. The generation of RNA alters the global phase behavior and organization of transcription components within condensates. Coarse-grained simulations of mesoscale structures at equilibrium show that the components stably assemble into multiphasic condensates and that the vesicles formed in vitro are the result of dynamical arrest. Overall, our findings illustrate the complex phase behavior of transcribing, multicomponent condensates, and they highlight the intimate, bidirectional interplay of structure and function in transcriptional condensates.
    Keywords:  biomolecular condensates; mitochondrial genome; phase separation; transcription; vesicles
    DOI:  https://doi.org/10.1073/pnas.2207303119
  26. Nat Commun. 2022 Oct 07. 13(1): 5918
    Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders.
    Junho Kim, August Yue Huang, Shelby L Johnson, Jenny Lai, Laura Isacco, Ailsa M Jeffries, Michael B Miller, Michael A Lodato, Christopher A Walsh, Eunjung Alice Lee.
      Replication errors and various genotoxins cause DNA double-strand breaks (DSBs) where error-prone repair creates genomic mutations, most frequently focal deletions, and defective repair may lead to neurodegeneration. Despite its pathophysiological importance, the extent to which faulty DSB repair alters the genome, and the mechanisms by which mutations arise, have not been systematically examined reflecting ineffective methods. Here, we develop PhaseDel, a computational method to detect focal deletions and characterize underlying mechanisms in single-cell whole genome sequences (scWGS). We analyzed high-coverage scWGS of 107 single neurons from 18 neurotypical individuals of various ages, and found that somatic deletions increased with age and in highly expressed genes in human brain. Our analysis of 50 single neurons from DNA repair-deficient diseases with progressive neurodegeneration (Cockayne syndrome, Xeroderma pigmentosum, and Ataxia telangiectasia) reveals elevated somatic deletions compared to age-matched controls. Distinctive mechanistic signatures and transcriptional associations suggest roles for somatic deletions in neurodegeneration.
    DOI:  https://doi.org/10.1038/s41467-022-33642-w
  27. Hum Cell. 2022 Oct 07.
    Hedgehog pathway is negatively regulated during the development of Drosophila melanogaster PheRS-m (Drosophila homologs gene of human FARS2) mutants.
    Lidangzhi Mo, Rui Li, Chunxia He, Qi Chen, Changwei Xu, Liangliang Shen, Kun Chen, Yuanming Wu.
      Hereditary spastic paraplegia (HSP) is a neurodegeneration disease, one of the reasons is caused by autosomal recessive missense mutation of the karyogene that encodes phenylalanyl-tRNA synthetase 2, mitochondrial (FARS2). However, the molecular mechanism underlying FARS2-mediated HSP progression is unknown. Mitochondrial phenylalanyl-tRNA synthetase gene (PheRS-m) is the Drosophila melanogaster homolog gene of human FARS2. This study constructed a Drosophila HSP missense mutation model and a PheRS-m knockout model. Some of the mutant fly phenotypes included developmental delay, shortened lifespan, wing-structure abnormalities and decreased mobility. RNA-sequencing results revealed a relationship between abnormal phenotypes and the hedgehog (Hh) pathway. A qRT-PCR assay was used to determine the key genes (ptc, hib, and slmb) of the Hh pathway that exhibited increased expression during different developmental stages. We demonstrated that Hh signaling transduction is negatively regulated during the developmental stages of PheRS-m mutants but positively regulated during adulthood. By inducing the agonist and inhibitor of Hh pathway in PheRS-m larvae, the developmental delay in mutants can be partly salvaged or postponed. Collectively, our findings indicate that Hh signaling negatively regulates the development of PheRS-m mutants, subsequently leading to developmental delay.
    Keywords:  Development; Drosophila melanogaster; Hedgehog pathway; Hereditary spastic paraplegia; PheRS-m
    DOI:  https://doi.org/10.1007/s13577-022-00796-0
  28. Nat Genet. 2022 Oct;54(10): 1504-1513
    Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements.
    Sofia Battaglia, Kevin Dong, Jingyi Wu, Zeyu Chen, Fadi J Najm, Yuanyuan Zhang, Molly M Moore, Vivian Hecht, Noam Shoresh, Bradley E Bernstein.
      Epigenomic maps identify gene regulatory elements by their chromatin state. However, prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate the interdependence of elements in a locus or capture single-molecule dynamics. Here, we apply targeted nanopore sequencing to profile chromatin accessibility and DNA methylation on contiguous ~100-kb DNA molecules that span loci relevant to development, immunity and imprinting. We detect promoters, enhancers, insulators and transcription factor footprints on single molecules based on exogenous GpC methylation. We infer relationships among dynamic elements within immune loci, and order successive remodeling events during T cell stimulation. Finally, we phase primary sequence and regulatory elements across the H19/IGF2 locus, uncovering primate-specific features. These include a segmental duplication that stabilizes the imprinting control region and a noncanonical enhancer that drives biallelic IGF2 expression in specific contexts. Our study advances emerging strategies for phasing gene regulatory landscapes and reveals a mechanism that overrides IGF2 imprinting in human cells.
    DOI:  https://doi.org/10.1038/s41588-022-01188-8
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