Biochemistry (Moscow)

, Volume 84, Issue 8, pp 884–895 | Cite as

DNA Replication in Human Mitochondria

  • L. A. ZinovkinaEmail author


DNA replication in human mitochondria has been studied for several decades; however, its mechanism still remains unclear. During the last 15 years, many new experimental data on the mitochondrial replication have appeared, although extremely contradictory. Two asynchronous (strand displacement and RITOLS) and one synchronous (strand coupled) replication models have been proposed. In the asynchronous models, replication from the origin in the H-chain starts earlier, so that the replication of the two chains ends at different times. The synchronous model is more traditional and implies two replication forks with leading and lagging strands initiated at the same origin. For each of the three models, both confirming and contradicting experimental data exist. Most likely, there is no single model of mitochondrial replication. It is possible that the unique mitochondrial replication machinery that has originated as a results of endosymbiosis has an unexpected variety of replication strategies to maintain the mitochondrial genome. An unusual combination of enzymes of different origin (phage, bacterial, eukaryotic) and unique features of the mitochondrial genome (existance of heavy and light chains, insertions of ribonucleotides, a variety of origins) can allow replication through different mechanisms. In human mitochondria, asynchronous replication seems to dominate; however, synchronous replication is also possible under certain conditions. In the human heart mitochondria, circular mitochondrial DNA (mtDNA) molecules can rearrange in a network of rapidly replicating linear genomes, thereby suggesting possible existence of a wide range of replication mechanisms in the mitochondria. The review describes the main stages of mtDNA replication and enzymes involved in this process, as well as discusses the prospects of mitochondrial replication studies.


mtDNA nucleoid D-loop replication strand displacement model RITOLS strand-coupled model 



conserved sequence block


heavy chain


light chain


mitochondrial genome maintenance exonuclease 1


mitochondrial DNA


non-coding region


heavy chain replication origin


light chain replication origin

ori b and ori z

origins b and z


DNA-directed RNA polymerase (mitochondrial)


RNA incorporated throughout the lagging strand


single-strand binding protein


termination-associated sequence


mitochondrial transcription elongation factor


transcription factor A of mitochondria


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The work was supported by the Russian Foundation for Basic Research (project 18-04-01110).

Conflict of interest. The author declares no conflict of interest.

Ethical norm compliance. This article does contain descriptions of the author’s studies with the participation of people and animals as research subjects.


  1. 1.
    Burger, G., Gray, M. W., and Lang, B. F. (2003) Mitochondrial genomes: anything goes, Trends Genet., 19, 709–716, doi: Scholar
  2. 2.
    Kolesnikov, A. A., and Gerasimov, E. S. (2012) Diversity of mitochondrial genome organization, Biochemistry (Moscow), 77, 1424–1435, doi: Scholar
  3. 3.
    Gualberto, J. M., Mileshina, D., Wallet, C., Niazi, A. K., Weber-Lotfi, F., and Dietrich, A. (2014) The plant mitochondrial genome: dynamics and maintenance, Biochimie, 100, 107–120, doi: Scholar
  4. 4.
    Sloan, D. B., Alverson, A. J., Chuckalovcak, J. P., Wu, M., McCauley, D. E., Palmer, J. D., and Taylor, D. R. (2012) Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates, PLoS Biol., 10, e1001241, doi: Scholar
  5. 5.
    Foury, F., Roganti, T., Lecrenier, N., and Purnelle, B. (1998) The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae, FEBS Lett., 440, 325–331, doi: Scholar
  6. 6.
    Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H., Coulson, A. R., Drouin, J., Eperon, I. C., Nierlich, D. P., Roe, B. A., Sanger, F., Schreier, P. H., Smith, A. J., Staden, R., and Young, I. G. (1981) Sequence and organization of the human mitochondrial genome, Nature, 290, 457–465, doi: Scholar
  7. 7.
    Pohjoismaki, J. L. O., and Goffart, S. (2011) Of circles, forks and humanity: topological organisation and replication of mammalian mitochondrial DNA, Bioessays, 33, 290–299, doi: Scholar
  8. 8.
    Pohjoismaki, J. L. O., Goffart, S., Tyynismaa, H., Willcox, S., Ide, T., Kang, D., Suomalainen, A., Karhunen, P. J., Griffith, J. D., Holt, I. J., and Jacobs, H. T. (2009) Human heart mitochondrial DNA is organized in complex catenated networks containing abundant four-way junctions and replication forks, J. Biol. Chem., 284, 21446–21457, doi: Scholar
  9. 9.
    Zinovkina, L. A. (2018) Mechanisms of mitochondrial DNA repair in mammals, Biochemistry (Moscow), 83, 233–249, doi: Scholar
  10. 10.
    Spelbrink, J. N. (2010) Functional organization of mammalian mitochondrial DNA in nucleoids: history, recent developments, and future challenges, IUBMB Life, 62, 19–32, doi: Scholar
  11. 11.
    Bogenhagen, D. F. (2012) Mitochondrial DNA nucleoid structure, Biochim. Biophys. Acta, 1819, 914–920, doi: Scholar
  12. 12.
    Brown, T. A., Tkachuk, A. N., Shtengel, G., Kopek, B. G., Bogenhagen, D. F., Hess, H. F., and Clayton, D. A. (2011) Super-resolution fluorescence imaging of mitochondrial nucleoids reveals their spatial range, limits, and membrane interaction, Mol. Cell. Biol., 31, 4994–5010, doi: Scholar
  13. 13.
    Kukat, C., Wurm, C. A., Spahr, H., Falkenberg, M., Larsson, N.-G., and Jakobs, S. (2011) Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA, Proc. Natl. Acad. Sci. USA, 108, 13534–12539, doi: Scholar
  14. 14.
    Lee, S. R., and Han, J. (2017) Mitochondrial nucleoid: shield and switch of the mitochondrial genome, Oxid. Med. Cell. Longev., 2017, 8060949, doi: Scholar
  15. 15.
    Bogenhagen, D. F., Rousseau, D., and Burke, S. (2008) The layered structure of human mitochondrial DNA nucleoids, J. Biol. Chem., 283, 3665–3675, doi: Scholar
  16. 16.
    Holt, I. J., He, J., Mao, C.-C., Boyd-Kirkup, J. D., Martinsson, P., Sembongi, H., Reyes, A., and Spelbrink, J. N. (2007) Mammalian mitochondrial nucleoids: organizing an independently minded genome, Mitochondrion, 7, 311–321, doi: Scholar
  17. 17.
    Hensen, F., Cansiz, S., Gerhold, J. M., and Spelbrink, J. N. (2014) To be or not to be a nucleoid protein: a comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins, Biochimie, 100, 219–226, doi: Scholar
  18. 18.
    Arnold, J. J., Smidansky, E. D., Moustafa, I. M., and Cameron, C. E. (2012) Human mitochondrial RNA polymerase: structure-function, mechanism and inhibition, Biochim. Biophys. Acta, 1819, 948–960, doi: Scholar
  19. 19.
    Ngo, H. B., Kaiser, J. T., and Chan, D. C. (2011) The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA, Nat. Struct. Mol. Biol., 18, 1290–1296, doi: Scholar
  20. 20.
    Agaronyan, K., Morozov, Y. I., Anikin, M., and Temiakov, D. (2015) Mitochondrial biology. Replication-transcription switch in human mitochondria, Science, 347, 548–551, doi: Scholar
  21. 21.
    Morozov, Y. I., Parshin, A. V., Agaronyan, K., Cheung, A. C. M., Anikin, M., Cramer, P., and Temiakov, D. (2015) A model for transcription initiation in human mitochondria, Nucleic Acids Res., 43, 3726–3735, doi: Scholar
  22. 22.
    Yin, Y. W. (2011) Structural insight on processivity, human disease and antiviral drug toxicity, Curr. Opin. Struct. Biol., 21, 83–91, doi: Scholar
  23. 23.
    Berglund, A.-K., Navarrete, C., Engqvist, M. K. M., Hoberg, E., Szilagyi, Z., Taylor, R. W., Gustafsson, C. M., Falkenberg, M., and Clausen, A. R. (2017) Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA, PLoS Genet., 13, e1006628, doi: Scholar
  24. 24.
    Kazak, L., Reyes, A., and Holt, I. J. (2012) Minimizing the damage: repair pathways keep mitochondrial DNA intact, Nat. Rev. Mol. Cell Biol., 13, 726–726, doi: Scholar
  25. 25.
    McKinney, E. A., and Oliveira, M. T. (2013) Replicating animal mitochondrial DNA, Genet. Mol. Biol., 36, 308–315, doi: Scholar
  26. 26.
    Satoh, M., and Kuroiwa, T. (1991) Organization of multiple nucleoids and DNA molecules in mitochondria of a human cell, Exp. Cell. Res., 196, 137–140, doi: Scholar
  27. 27.
    Iborra, F. J., Kimura, H., and Cook, P. R. (2004) The functional organization of mitochondrial genomes in human cells, BMC Biol., 2, 9, doi: Scholar
  28. 28.
    Legros, F., Malka, F., Frachon, P., Lombes, A., and Rojo, M. (2004) Organization and dynamics of human mitochondrial DNA, J. Cell Sci., 117, 2653–2662, doi: Scholar
  29. 29.
    Gilkerson, R. W., Schon, E. A., Hernandez, E., and Davidson, M. M. (2008) Mitochondrial nucleoids maintain genetic autonomy but allow for functional complementation, J. Cell. Biol., 181, 1117–1128, doi: Scholar
  30. 30.
    Van Blerkom, J. (2011) Mitochondrial function in the human oocyte and embryo and their role in developmental competence, Mitochondrion, 11, 797–813, doi: Scholar
  31. 31.
    Kaufman, B. A., Durisic, N., Mativetsky, J. M., Costantino, S., Hancock, M. A., Grutter, P., and Shoubridge, E. A. (2007) The mitochondrial transcription factor TFAM coordinates the assembly of multiple DNA molecules into nucleoid-like structures, Mol. Biol. Cell, 18, 3225–3236, doi: Scholar
  32. 32.
    Farge, G., Mehmedovic, M., Baclayon, M., van den Wildenberg, S. M. J. L., Roos, W. H., Gustafsson, C. M., Wuite, G. J. L., and Falkenberg, M. (2014) In vitro-reconstituted nucleoids can block mitochondrial DNA replication and transcription, Cell Rep., 8, 66–74, doi: Scholar
  33. 33.
    Kukat, C., Davies, K. M., Wurm, C. A., Spahr, H., Bonekamp, N. A., Kuhl, I., Joos, F., Polosa, P. L., Park, C. B., Posse, V., Falkenberg, M., Jakobs, S., Kuhlbrandt, W., and Larsson, N.-G. (2015) Cross-strand binding of TFAM to a single mtDNA molecule forms the mitochondrial nucleoid, Proc. Natl. Acad. Sci. USA, 112, 11288–11293, doi: Scholar
  34. 34.
    Falkenberg, M. (2018) Mitochondrial DNA replication in mammalian cells: overview of the pathway, Essays Biochem., 62, 287–296, doi: Scholar
  35. 35.
    Lewis, S. C., Uchiyama, L. F., and Nunnari, J. (2016) ER-mitochondria contacts couple mtDNA synthesis with mitochondrial division in human cells, Science, 353, 5549, doi: Scholar
  36. 36.
    Malka, F., Lombes, A., and Rojo, M. (2006) Organization, dynamics and transmission of mitochondrial DNA: focus on vertebrate nucleoids, Biochim. Biophys. Acta, 1763, 463–472, doi: Scholar
  37. 37.
    Wang, J., Schmitt, E. S., Landsverk, M. L., Zhang, V. W., Li, F.-Y., Graham, B. H., Craigen, W. J., and Wong, L.-J. C. (2012) An integrated approach for classifying mitochondrial DNA variants: one clinical diagnostic laboratory’s experience, Genet. Med., 14, 620–626, doi: Scholar
  38. 38.
    D’Aurelio, M., Gajewski, C. D., Lin, M. T., Mauck, W. M., Shao, L. Z., Lenaz, G., Moraes, C. T., and Manfredi, G. (2004) Heterologous mitochondrial DNA recombination in human cells, Hum. Mol. Genet., 13, 3171–3179, doi: Scholar
  39. 39.
    Kennedy, S. R., Salk, J. J., Schmitt, M. W., and Loeb, L. A. (2013) Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage, PLoS Genet., 9, e1003794, doi: Scholar
  40. 40.
    Nicholls, T. J., and Minczuk, M. (2014) In D-loop: 40 years of mitochondrial 7S DNA, Exp. Gerontol., 56, 175–181, doi: Scholar
  41. 41.
    Arnberg, A., van Bruggen, E. F., and Borst, P. (1971) The presence of DNA molecules with a displacement loop in standard mitochondrial DNA preparations, Biochim. Biophys. Acta, 246, 353–357, doi: Scholar
  42. 42.
    Jemt, E., Persson, O., Shi, Y., Mehmedovic, M., Uhler, J. P., Davila Lopez, M., Freyer, C., Gustafsson, C. M., Samuelsson, T., and Falkenberg, M. (2015) Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element, Nucleic Acids Res., 43, 9262–9275, doi: Scholar
  43. 43.
    Robberson, D. L., Kasamatsu, H., and Vinograd, J. (1972) Replication of mitochondrial DNA. Circular replicative intermediates in mouse L cells, Proc. Natl. Acad. Sci. USA, 69, 737–741.CrossRefGoogle Scholar
  44. 44.
    Fuste, J. M., Wanrooij, S., Jemt, E., Granycome, C. E., Cluett, T. J., Shi, Y., Atanassova, N., Holt, I. J., Gustafsson, C. M., and Falkenberg, M. (2010) Mitochondrial RNA polymerase is needed for activation of the origin of light-strand DNA replication, Mol. Cell, 37, 67–78, doi: Scholar
  45. 45.
    Yasukawa, T., and Kang, D. (2018) An overview of mammalian mitochondrial DNA replication mechanisms, J. Biochem., 164, 183–193, doi: Scholar
  46. 46.
    Holt, I. J., Lorimer, H. E., and Jacobs, H. T. (2000) Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA, Cell, 100, 515–524, doi: Scholar
  47. 47.
    Bowmaker, M., Yang, M. Y., Yasukawa, T., Reyes, A., Jacobs, H. T., Huberman, J. A., and Holt, I. J. (2003) Mammalian mitochondrial DNA replicates bidirectionally from an initiation zone, J. Biol. Chem., 278, 50961–50969, doi: Scholar
  48. 48.
    Holt, I. J., and Jacobs, H. T. (2014) Unique features of DNA replication in mitochondria: a functional and evolutionary perspective, Bioessays, 36, 1024–1031, doi: Scholar
  49. 49.
    Yang, M. Y., Bowmaker, M., Reyes, A., Vergani, L., Angeli, P., Gringeri, E., Jacobs, H. T., and Holt, I. J. (2002) Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication, Cell, 111, 495–505, doi: Scholar
  50. 50.
    Yasukawa, T., Reyes, A., Cluett, T. J., Yang, M.-Y., Bowmaker, M., Jacobs, H. T., and Holt, I. J. (2006) Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand, EMBO J., 25, 5358–5371, doi: Scholar
  51. 51.
    Yasukawa, T., Yang, M.-Y., Jacobs, H. T., and Holt, I. J. (2005) A bidirectional origin of replication maps to the major noncoding region of human mitochondrial DNA, Mol. Cell, 18, 651–662, doi: Scholar
  52. 52.
    Reyes, A., Kazak, L., Wood, S. R., Yasukawa, T., Jacobs, H. T., and Holt, I. J. (2013) Mitochondrial DNA replication proceeds via a “bootlace” mechanism involving the incorporation of processed transcripts, Nucleic Acids Res., 41, 5837–5850, doi: Scholar
  53. 53.
    Bogenhagen, D. F., and Clayton, D. A. (2003) The mitochondrial DNA replication bubble has not burst, Trends Biochem. Sci., 28, 357–360, doi: Scholar
  54. 54.
    Bogenhagen, D. F., and Clayton, D. A. (2003) Concluding remarks: The mitochondrial DNA replication bubble has not burst, Trends Biochem. Sci., 28, 404–405, doi: Scholar
  55. 55.
    Holt, I. J., and Jacobs, H. T. (2003) Response: The mitochondrial DNA replication bubble has not burst, Trends Biochem. Sci., 28, 355–356, doi: Scholar
  56. 56.
    Pohjoismaki, J. L. O., Holmes, J. B., Wood, S. R., Yang, M.-Y., Yasukawa, T., Reyes, A., Bailey, L. J., Cluett, T. J., Goffart, S., Willcox, S., Rigby, R. E., Jackson, A. P., Spelbrink, J. N., Griffith, J. D., Crouch, R. J., Jacobs, H. T., and Holt, I. J. (2010) Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid, J. Mol. Biol., 397, 1144–1155, doi: Scholar
  57. 57.
    Miralles Fuste, J., Shi, Y., Wanrooij, S., Zhu, X., Jemt, E., Persson, O., Sabouri, N., Gustafsson, C. M., and Falkenberg, M. (2014) In vivo occupancy of mitochondrial single-stranded DNA binding protein supports the strand displacement mode of DNA replication, PLoS Genet., 10, e1004832, doi: Scholar
  58. 58.
    Phillips, A. F., Millet, A. R., Tigano, M., Dubois, S. M., Crimmins, H., Babin, L., Charpentier, M., Piganeau, M., Brunet, E., and Sfeir, A. (2017) Single-molecule analysis of mtDNA replication uncovers the basis of the common deletion, Mol. Cell, 65, 527–538, doi: Scholar
  59. 59.
    Holmes, J. B., Akman, G., Wood, S. R., Sakhuja, K., Cerritelli, S. M., Moss, C., Bowmaker, M. R., Jacobs, H. T., Crouch, R. J., and Holt, I. J. (2015) Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication, Proc. Natl. Acad. Sci. USA, 112, 9334–9339, doi: Scholar
  60. 60.
    Wanrooij, S., Miralles Fuste, J., Stewart, J. B., Wanrooij, P. H., Samuelsson, T., Larsson, N.-G., Gustafsson, C. M., and Falkenberg, M. (2012) In vivo mutagenesis reveals that OriL is essential for mitochondrial DNA replication, EMBO Rep., 13, 1130–1137, doi: Scholar
  61. 61.
    Khaidakov, M. (2016) Species-specific lifespans: can it be a lottery based on the mode of mitochondrial DNA replication? Mech. Ageing Dev., 155, 1–6, doi: Scholar
  62. 62.
    Lakshmipathy, U., and Campbell, C. (1999) The human DNA ligase III gene encodes nuclear and mitochondrial proteins, Mol. Cell. Biol., 19, 3869–3876.CrossRefGoogle Scholar
  63. 63.
    Puebla-Osorio, N., Lacey, D. B., Alt, F. W., and Zhu, C. (2006) Early embryonic lethality due to targeted inactivation of DNA ligase III, Mol. Cell. Biol., 26, 3935–3941, doi: Scholar
  64. 64.
    Cerritelli, S. M., Frolova, E. G., Feng, C., Grinberg, A., Love, P. E., and Crouch, R. J. (2003) Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice, Mol. Cell, 11, 807–815, doi: Scholar
  65. 65.
    Macao, B., Uhler, J. P., Siibak, T., Zhu, X., Shi, Y., Sheng, W., Olsson, M., Stewart, J. B., Gustafsson, C. M., and Falkenberg, M. (2015) The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication, Nat. Commun., 6, 7303, doi: Scholar
  66. 66.
    Trifunovic, A., Wredenberg, A., Falkenberg, M., Spelbrink, J. N., Rovio, A. T., Bruder, C. E., Bohlooly, Y. M., Gidlof, S., Oldfors, A., Wibom, R., Tornell, J., Jacobs, H. T., and Larsson, N.-G. (2004) Premature ageing in mice expressing defective mitochondrial DNA polymerase, Nature, 429, 417–423, doi: Scholar
  67. 67.
    Nicholls, T. J., Zsurka, G., Peeva, V., Scholer, S., Szczesny, R. J., Cysewski, D., Reyes, A., Kornblum, C., Sciacco, M., Moggio, M., Dziembowski, A., Kunz, W. S., and Minczuk, M. (2014) Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease, Hum. Mol. Genet., 23, 6147–6162, doi: Scholar
  68. 68.
    Kornblum, C., Nicholls, T. J., Haack, T. B., Scholer, S., Peeva, V., Danhauser, K., Hallmann, K., Zsurka, G., Rorbach, J., Iuso, A., Wieland, T., Sciacco, M., Ronchi, D., Comi, G. P., Moggio, M., Quinzii, C. M., DiMauro, S., Calvo, S. E., Mootha, V. K., Klopstock, T., Strom, T. M., Meitinger, T., Minczuk, M., Kunz, W. S., and Prokisch, H. (2013) Loss-of-function mutations in MGME1 impair mtDNA replication and cause multisystemic mitochondrial disease, Nat. Genet., 45, 214–219, doi: Scholar
  69. 69.
    Stewart, L., Redinbo, M. R., Qiu, X., Hol, W. G., and Champoux, J. J. (1998) A model for the mechanism of human topoisomerase I, Science, 279, 1534–1541, doi: Scholar
  70. 70.
    Douarrure, C., Sobier, C., Dalla Rosa, I., Brata Das, B., Redon, C. E., Zhang, H., Neckers, L., and Pommier, Y. (2012) Mitochondrial topoisomerase I is critical for mitochondrial integrity and cellular energy metabolism, PLoS One, 7, e41094, doi: Scholar
  71. 71.
    Zhang, H., Zhang, Y.-W., Yasukawa, T., Dalla Rosa, I., Khiati, S., and Pommier, Y. (2014) Increased negative supercoiling of mtDNA in TOP1mt knockout mice and presence of topoisomerases IIα and IIβ in vertebrate mitochondria, Nucleic Acids Res., 42, 7259–7267, doi: Scholar
  72. 72.
    Nicholls, T. J., Nadalutti, C. A., Motori, E., Sommerville, E. W., Gorman, G. S., Basu, S., Hoberg, E., Turnbull, D. M., Chinnery, P. F., Larsson, N.-G., Larsson, E., Falkenberg, M., Taylor, R. W., Griffith, J. D., and Gustafsson, C. M. (2018) Topoisomerase 3α is required for decatenation and segregation of human mtDNA, Mol. Cell, 69, 9–23, doi: Scholar
  73. 73.
    Huynen, M. A., Duarte, I., and Szklarczyk, R. (2013) Loss, replacement and gain of proteins at the origin of the mitochondria, Biochim. Biophys. Acta, 1827, 224–231, doi: Scholar
  74. 74.
    Shutt, T. E., and Gray, M. W. (2006) Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont, Mol. Biol. Evol., 23, 1169–1179, doi: Scholar

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© Pleiades Publishing, Ltd. 2019

Authors and Affiliations

  1. 1.Lomonosov Moscow State University, Faculty of Bioengineering and BioinformaticsMoscowRussia

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