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  • Review Article
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes

Nature Reviews Molecular Cell Biology volume 24, pages 414–429 (2023)Cite this article

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Abstract

One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid–liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.

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Fig. 1: rDNA organization and recombination in budding yeast.
Fig. 2: Organization of the ribosomal rRNA gene in human cells.
Fig. 3: Outline of the RNA polymerase I transcription process.
Fig. 4: Regulation of rDNA transcription by heterochromatin formation through DNA methylation and histone modifications.
Fig. 5: Functional organization of the nucleolus.

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References

  1. Nomura, M., Morgan, E. A. & Jaskunas, S. R. Genetics of bacterial ribosomes. Annu. Rev. Genet. 11, 297–347 (1977).

    Article  CAS  PubMed  Google Scholar 

  2. Warner, J. R. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24, 437–440 (1999).

    Article  CAS  PubMed  Google Scholar 

  3. Kobayashi, T. Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast. Cell. Mol. Life Sci. 68, 1395–1403 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Long, E. O. & Dawid, I. B. Repeated genes in eukaryotes. Annu. Rev. Biochem. 49, 727–764 (1980).

    Article  CAS  PubMed  Google Scholar 

  5. Kobayashi, T. A new role of the rDNA and nucleolus in the nucleus — rDNA instability maintains genome integrity. Bioessays 30, 267–272 (2008).

    Article  CAS  PubMed  Google Scholar 

  6. Brewer, B. J. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 53, 679–686 (1988).

    Article  CAS  PubMed  Google Scholar 

  7. Mirkin, E. V. & Mirkin, S. M. Mechanisms of transcription-replication collisions in bacteria. Mol. Cell. Biol. 25, 888–895 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Horiuchi, T., Hidaka, M. & Kobayashi, T. Termination of chromosome duplication in bacteria in Control of Cell Growth and Division (Japan Scientific Societies Press, Springer-Verlag, 1991).

  9. Petes, T. D. Yeast ribosomal DNA genes are located on chromosome XII. Proc. Natl Acad. Sci. USA 76, 410–414 (1979).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Kobayashi, T., Heck, D. J., Nomura, M. & Horiuchi, T. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev. 12, 3821–3830 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ganley, A. R. D. & Kobayashi, T. Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res. 17, 184–191 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Dieci, G., Fiorino, G., Castelnuovo, M., Teichmann, M. & Pagano, A. The expanding RNA polymerase III transcriptome. Trends Genet. 23, 614–622 (2007).

    Article  CAS  PubMed  Google Scholar 

  13. Kobayashi, T. Ribosomal RNA gene repeats, their stability and cellular senescence. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 90, 119–129 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Brewer, B. J. & Fangman, W. L. A replication fork barrier at the 3’ end of yeast ribosomal RNA genes. Cell 55, 637–643 (1988).

    Article  CAS  PubMed  Google Scholar 

  15. Linskens, M. H. & Huberman, J. A. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8, 4927–4935 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Brewer, B. J., Lockshon, D. & Fangman, W. L. The arrest of replication forks in the rDNA of yeast occurs independently of transcription. Cell 71, 267–276 (1992).

    Article  CAS  PubMed  Google Scholar 

  17. Kobayashi, T., Hidaka, M., Nishizawa, M. & Horiuchi, T. Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae. Mol. Gen. Genet. 233, 355–362 (1992).

    Article  CAS  PubMed  Google Scholar 

  18. Kobayashi, T. The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork. Mol. Cell. Biol. 23, 9178–9188 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hizume, K., Endo, S., Muramatsu, S., Kobayashi, T. & Araki, H. DNA polymerase ε-dependent modulation of the pausing property of the CMG helicase at the barrier. Genes Dev. 32, 1315–1320 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Weitao, T., Budd, M. & Campbell, J. L. Evidence that yeast SGS1, DNA2, SRS2, and FOB1 interact to maintain rDNA stability. Mutat. Res. Mol. Mech. Mutagen. 532, 157–172 (2003).

    Article  CAS  Google Scholar 

  21. Burkhalter, M. D. & Sogo, J. M. rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication. Mol. Cell 15, 409–421 (2004).

    Article  CAS  PubMed  Google Scholar 

  22. Kobayashi, T., Horiuchi, T., Tongaonkar, P., Vu, L. & Nomura, M. SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast. Cell 117, 441–453 (2004).

    Article  CAS  PubMed  Google Scholar 

  23. Sasaki, M. & Kobayashi, T. Ctf4 prevents genome rearrangements by suppressing DNA double-strand break formation and its end resection at arrested replication forks. Mol. Cell 66, 533–545.e5 (2017).

    Article  CAS  PubMed  Google Scholar 

  24. Kobayashi, T. & Ganley, A. R. D. Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 309, 1581–1584 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Kobayashi, T., Nomura, M. & Horiuchi, T. Identification of DNA cis elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae. Mol. Cell. Biol. 21, 136–147 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Santangelo, G. M., Tornow, J., McLaughlin, C. S. & Moldave, K. Properties of promoters cloned randomly from the Saccharomyces cerevisiae genome. Mol. Cell. Biol. 8, 4217–4224 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Saka, K., Ide, S., Ganley, A. R. D. & Kobayashi, T. Cellular senescence in yeast is regulated by rDNA noncoding transcription. Curr. Biol. 23, 1794–1798 (2013).

    Article  CAS  PubMed  Google Scholar 

  28. Iida, T. & Kobayashi, T. RNA polymerase I activators count and adjust ribosomal RNA gene copy number. Mol. Cell 73, 645–654 (2019).

    Article  CAS  PubMed  Google Scholar 

  29. Keener, J., Josaitis, C. A., Dodd, J. A. & Nomura, M. Reconstitution of yeast RNA polymerase I transcription in vitro from purified components. TATA-binding protein is not required for basal transcription. J. Biol. Chem. 273, 33795–33802 (1998).

    Article  CAS  PubMed  Google Scholar 

  30. Vu, L., Siddiqi, I., Lee, B. S., Josaitis, C. A. & Nomura, M. RNA polymerase switch in transcription of yeast rDNA: role of transcription factor UAF (upstream activation factor) in silencing rDNA transcription by RNA polymerase II. Proc. Natl Acad. Sci. USA 96, 4390–4395 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Florence, B. et al. Mechanism of RNA polymerase I selection by transcription factor UAF. Sci. Adv. 8, eabn5725 (2022).

    Article  Google Scholar 

  32. Siddiqi, I. N. et al. Transcription of chromosomal rRNA genes by both RNA polymerase I and II in yeast uaf30 mutants lacking the 30 kDa subunit of transcription factor UAF. EMBO J. 20, 4512–4521 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N. & Mann, M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat. Methods 11, 319–324 (2014).

    Article  CAS  PubMed  Google Scholar 

  34. Iida, T. & Kobayashi, T. How do cells count multi-copy genes?: “musical chair” model for preserving the number of rDNA copies. Curr. Genet. 65, 883–885 (2019).

    Article  CAS  PubMed  Google Scholar 

  35. Sinclair, D. A. & Guarente, L. Extrachromosomal rDNA circles - A cause of aging in yeast. Cell 91, 1033–1042 (1997).

    Article  CAS  PubMed  Google Scholar 

  36. van Sluis, M. et al. Human NORs, comprising rDNA arrays and functionally conserved distal elements, are located within dynamic chromosomal regions. Genes Dev. 33, 1688–1701 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Gerber, J.-K. et al. Termination of mammalian rDNA replication: polar arrest of replication fork movement by transcription termination factor TTF-I. Cell 90, 559–567 (1997).

    Article  CAS  PubMed  Google Scholar 

  38. Akamatsu, Y. & Kobayashi, T. The human RNA polymerase I transcription terminator complex acts as a replication fork barrier that coordinates the progress of replication with rRNA transcription activity. Mol. Cell. Biol. 35, 1871–1881 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. De Winter, R. F. & Moss, T. The ribosomal spacer in Xenopus laevis is transcribed as part of the primary ribosomal RNA. Nucleic Acids Res. 14, 6041–6051 (1986).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Kuhn, A. & Grummt, I. A novel promoter in the mouse rDNA spacer is active in vivo and in vitro. EMBO J. 6, 3487–3492 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Mayer, C., Schmitz, K.-M., Li, J., Grummt, I. & Santoro, R. Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol. Cell 22, 351–361 (2006).

    Article  CAS  PubMed  Google Scholar 

  42. Hori, Y., Shimamoto, A. & Kobayashi, T. The human ribosomal DNA array is composed of highly homogenized tandem clusters. Genome Res. 31, 1971–1982 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Parks, M. M. et al. Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression. Sci. Adv. 4, eaao0665 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  44. Stults, D. M. et al. Human rRNA gene clusters are recombinational hotspots in cancer. Cancer Res. 69, 9096–9104 (2009).

    Article  CAS  PubMed  Google Scholar 

  45. Killen, M. W., Stults, D. M., Adachi, N., Hanakahi, L. & Pierce, A. J. Loss of Bloom syndrome protein destabilizes human gene cluster architecture. Hum. Mol. Genet. 18, 3417–3428 (2009).

    Article  CAS  PubMed  Google Scholar 

  46. Milkereit, P. & Tschochner, H. A specialized form of RNA polymerase I, essential for initiation and growth-dependent regulation of rRNA synthesis, is disrupted during transcription. EMBO J. 17, 3692–3703 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Buttgereit, D., Pflugfelder, G. & Grummt, I. Growth-dependent regulation of rRNA synthesis is mediated by a transcription initiation factor (TTF-IA). Nucleic Acids Res. 13, 8165–8180 (1985).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Yamamoto, R. T., Nogi, Y., Dodd, J. A. & Nomura, M. RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J. 15, 3964–3973 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Miller, G. et al. hRRN3 is essential in the SL1‐mediated recruitment of RNA polymerase I to rRNA gene promoters. EMBO J. 20, 1373–1382 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Moorefield, B., Greene, E. A. & Reeder, R. H. RNA polymerase I transcription factor Rrn3 is functionally conserved between yeast and human. Proc. Natl Acad. Sci. USA 97, 4724–4729 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Learned, R. M., Cordes, S. & Tjian, R. Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I. Mol. Cell. Biol. 5, 1358–1369 (1985).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Russell, J. & Zomerdijk, J. C. B. M. The RNA polymerase I transcription machinery. Biochem. Soc. Symp. https://doi.org/10.1042/bss0730203 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  53. Moss, T., Langlois, F., Gagnon-Kugler, T. & Stefanovsky, V. A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis. Cell. Mol. Life Sci. 64, 29–49 (2007).

    Article  CAS  PubMed  Google Scholar 

  54. Keys, D. A. et al. Multiprotein transcription factor UAF interacts with the upstream element of the yeast RNA polymerase I promoter and forms a stable preinitiation complex. Genes Dev. 10, 887–903 (1996).

    Article  CAS  PubMed  Google Scholar 

  55. Vannini, A. & Cramer, P. Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol. Cell 45, 439–446 (2012).

    Article  CAS  PubMed  Google Scholar 

  56. Miller, O. L. J. & Beatty, B. R. Visualization of nucleolar genes. Science 164, 955–957 (1969).

    Article  PubMed  Google Scholar 

  57. Lisica, A. et al. Mechanisms of backtrack recovery by RNA polymerases I and II. Proc. Natl Acad. Sci. USA 113, 2946–2951 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Kuhn, C.-D. et al. Functional architecture of RNA polymerase I. Cell 131, 1260–1272 (2007).

    Article  CAS  PubMed  Google Scholar 

  59. Engel, C., Sainsbury, S., Cheung, A. C., Kostrewa, D. & Cramer, P. RNA polymerase I structure and transcription regulation. Nature 502, 650–655 (2013).

    Article  CAS  PubMed  Google Scholar 

  60. Fernández-Tornero, C. et al. Crystal structure of the 14-subunit RNA polymerase I. Nature 502, 644–649 (2013).

    Article  PubMed  Google Scholar 

  61. Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863–1876 (2001).

    Article  CAS  PubMed  Google Scholar 

  62. Jennebach, S., Herzog, F., Aebersold, R. & Cramer, P. Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage. Nucleic Acids Res. 40, 5591–5601 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Scull, C. E., Lucius, A. L. & Schneider, D. A. The N-terminal domain of the A12.2 subunit stimulates RNA polymerase I transcription elongation. Biophys. J. 120, 1883–1893 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Van Mullem, V., Landrieux, E., Vandenhaute, J. & Thuriaux, P. Rpa12p, a conserved RNA polymerase I subunit with two functional domains. Mol. Microbiol. 43, 1105–1113 (2002).

    Article  PubMed  Google Scholar 

  65. Geiger, S. R. et al. RNA polymerase I contains a TFIIF-related DNA-binding subcomplex. Mol. Cell 39, 583–594 (2010).

    Article  CAS  PubMed  Google Scholar 

  66. Darrière, T. et al. Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I. PLoS Genet. 15, e1008157 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  67. Pilsl, M. et al. Structure of the initiation-competent RNA polymerase I and its implication for transcription. Nat. Commun. 7, 12126 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Han, Y. et al. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. Elife 6, e27414 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  69. Sadian, Y. et al. Molecular insight into RNA polymerase I promoter recognition and promoter melting. Nat. Commun. 10, 5543 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Heiss, F. B., Daiß, J. L., Becker, P. & Engel, C. Conserved strategies of RNA polymerase I hibernation and activation. Nat. Commun. 12, 758 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Torreira, E. et al. The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription. Elife 6, e20832 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Milkereit, P., Schultz, P. & Tschochner, H. Resolution of RNA polymerase I into dimers and monomers and their function in transcription. Biol. Chem. 378, 1433–1443 (1997).

    Article  CAS  PubMed  Google Scholar 

  73. Bischler, N. et al. Localization of the yeast RNA polymerase I-specific subunits. EMBO J. 21, 4136–4144 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Sanz-Murillo, M. et al. Structural basis of RNA polymerase I stalling at UV light-induced DNA damage. Proc. Natl Acad. Sci. USA 115, 8972–8977 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Jacobs, R. Q., Ingram, Z. M., Lucius, A. L. & Schneider, D. A. Defining the divergent enzymatic properties of RNA polymerases I and II. J. Biol. Chem. 296, 100051 (2021).

    Article  CAS  PubMed  Google Scholar 

  76. Daiß, J. L. et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Sci. Alliance 5, e202201568 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Engel, C., Neyer, S. & Cramer, P. Distinct mechanisms of transcription initiation by RNA polymerases I and II. Annu. Rev. Biophys. 47, 425–446 (2018).

    Article  CAS  PubMed  Google Scholar 

  78. Engel, C. et al. Structural basis of RNA polymerase I transcription initiation. Cell 169, 120–131.e22 (2017).

    Article  CAS  PubMed  Google Scholar 

  79. Sadian, Y. et al. Structural insights into transcription initiation by yeast RNA polymerase I. EMBO J. 36, 2698–2709 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Fernández-Tornero, C. RNA polymerase I activation and hibernation: unique mechanisms for unique genes. Transcription 9, 248–254 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  81. Neyer, S. et al. Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature 540, 607–610 (2016).

    Article  CAS  PubMed  Google Scholar 

  82. Tafur, L. et al. Molecular structures of transcribing RNA polymerase I. Mol. Cell 64, 1135–1143 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Pilsl, M. & Engel, C. Structural basis of RNA polymerase I pre-initiation complex formation and promoter melting. Nat. Commun. 11, 1206 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Kulkens, T., Riggs, D. L., Heck, J. D., Planta, R. J. & Nomura, M. The yeast RNA polymerase I promoter: ribosomal DNA sequences involved in transcription initiation and complex formation in vitro. Nucleic Acids Res. 19, 5363–5370 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Kownin, P., Bateman, E. & Paule, M. R. Eukaryotic RNA polymerase I promoter binding is directed by protein contacts with transcription initiation factor and is DNA sequence-independent. Cell 50, 693–699 (1987).

    Article  CAS  PubMed  Google Scholar 

  86. Abascal-Palacios, G., Ramsay, E. P., Beuron, F., Morris, E. & Vannini, A. Structural basis of RNA polymerase III transcription initiation. Nature 553, 301–306 (2018).

    Article  CAS  PubMed  Google Scholar 

  87. Vorländer, M. K., Khatter, H., Wetzel, R., Hagen, W. J. H. & Müller, C. W. Molecular mechanism of promoter opening by RNA polymerase III. Nature 553, 295–300 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  88. Aibara, S., Schilbach, S. & Cramer, P. Structures of mammalian RNA polymerase II pre-initiation complexes. Nature 594, 124–128 (2021).

    Article  CAS  PubMed  Google Scholar 

  89. Schilbach, S., Aibara, S., Dienemann, C., Grabbe, F. & Cramer, P. Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. Cell 184, 4064–4072.e28 (2021).

    Article  CAS  PubMed  Google Scholar 

  90. Nikolov, D. B. et al. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377, 119–128 (1995).

    Article  CAS  PubMed  Google Scholar 

  91. Knutson, B. A. & Hahn, S. Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors. Science 333, 1637–1640 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Naidu, S., Friedrich, J. K., Russell, J. & Zomerdijk, J. C. B. M. TAF1B is a TFIIB-like component of the basal transcription machinery for RNA polymerase I. Science 333, 1640–1642 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. French, S. L., Osheim, Y. N., Cioci, F., Nomura, M. & Beyer, A. L. In exponentially growing saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol. Cell. Biol. 23, 1558–1568 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Kessler, A. C. & Maraia, R. J. The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance. Nucleic Acids Res. 49, 12017–12034 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Wang, Q., Daiß, J. L., Xu, Y. & Engel, C. Snapshots of RNA polymerase III in action - a mini review. Gene 821, 146282 (2022).

    Article  CAS  PubMed  Google Scholar 

  96. Girbig, M., Misiaszek, A. D. & Müller, C. W. Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases. Nat. Rev. Mol. Cell Biol. 23, 603–622 (2022).

    Article  CAS  PubMed  Google Scholar 

  97. Vannini, A. et al. Molecular basis of RNA polymerase III transcription repression by Maf1. Cell 143, 59–70 (2010).

    Article  CAS  PubMed  Google Scholar 

  98. Vorländer, M. K. et al. Structural basis for RNA polymerase III transcription repression by Maf1. Nat. Struct. Mol. Biol. 27, 229–232 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  99. Michels, A. A. et al. mTORC1 directly phosphorylates and regulates human MAF1. Mol. Cell. Biol. 30, 3749–3757 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Shor, B. et al. Requirement of the mTOR kinase for the regulation of Maf1 phosphorylation and control of RNA polymerase III-dependent transcription in cancer cells. J. Biol. Chem. 285, 15380–15392 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Liu, G. Y. & Sabatini, D. M. mTOR at the nexus of nutrition, growth, ageing and disease. Nat. Rev. Mol. Cell Biol. 21, 183–203 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Mayer, C., Zhao, J., Yuan, X. & Grummt, I. mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev. 18, 423–434 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Hannan, K. M. et al. mTOR-dependent regulation of ribosomal gene transcription requires S6K1 and is mediated by phosphorylation of the carboxy-terminal activation domain of the nucleolar transcription factor UBF. Mol. Cell. Biol. 23, 8862–8877 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Claypool, J. A. et al. Tor pathway regulates Rrn3p-dependent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol. Biol. Cell 15, 946–956 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Ben-Sahra, I., Hoxhaj, G., Ricoult, S. J. H., Asara, J. M. & Manning, B. D. mTORC1 induces purine synthesis through control of the mitochondrial tetrahydrofolate cycle. Science 351, 728–733 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Robitaille, A. M. et al. Quantitative phosphoproteomics reveal mTORC1 activates de novo pyrimidine synthesis. Science 339, 1320–1323 (2013).

    Article  CAS  PubMed  Google Scholar 

  107. Ben-Sahra, I., Howell, J. J., Asara, J. M. & Manning, B. D. Stimulation of de novo pyrimidine synthesis by growth signaling through mTOR and S6K1. Science 339, 1323–1328 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Düvel, K. et al. Activation of a metabolic gene regulatory network downstream of mTOR complex 1. Mol. Cell 39, 171–183 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  109. Schnapp, A., Schnapp, G., Erny, B. & Grummt, I. Function of the growth-regulated transcription initiation factor TIF-IA in initiation complex formation at the murine ribosomal gene promoter. Mol. Cell. Biol. 13, 6723–6732 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Zhao, J., Yuan, X., Frödin, M. & Grummt, I. ERK-dependent phosphorylation of the transcription initiation factor TIF-IA is required for RNA polymerase I transcription and cell growth. Mol. Cell 11, 405–413 (2003).

    Article  CAS  PubMed  Google Scholar 

  111. Blattner, C. et al. Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev. 25, 2093–2105 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Engel, C., Plitzko, J. & Cramer, P. RNA polymerase I–Rrn3 complex at 4.8 Å resolution. Nat. Commun. 7, 12129 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Misiaszek, A. D. et al. Cryo-EM structures of human RNA polymerase I. Nat. Struct. Mol. Biol. 28, 997–1008 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Bierhoff, H., Dundr, M., Michels, A. A. & Grummt, I. Phosphorylation by casein kinase 2 facilitates rRNA gene transcription by promoting dissociation of TIF-IA from elongating RNA polymerase I. Mol. Cell. Biol. 28, 4988–4998 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Rothblum, K., Hu, Q., Penrod, Y. & Rothblum, L. I. Selective inhibition of rDNA transcription by a small-molecule peptide that targets the interface between RNA polymerase I and Rrn3. Mol. Cancer Res. 12, 1586–1596 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Gerber, J. et al. Site specific phosphorylation of yeast RNA polymerase I. Nucleic Acids Res. 36, 793–802 (2008).

    Article  CAS  PubMed  Google Scholar 

  117. Stephan, F. et al. Differential roles of phosphorylation in the formation of transcriptional active RNA polymerase I. Proc. Natl Acad. Sci. USA 98, 14334–14339 (2001).

    Article  Google Scholar 

  118. Clemente-Blanco, A. et al. Cdc14 inhibits transcription by RNA polymerase I during anaphase. Nature 458, 219–222 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Rodriguez-Algarra, F. et al. Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states. Genome Biol. 23, 54 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. McStay, B. & Grummt, I. The epigenetics of rRNA genes: from molecular to chromosome biology. Annu. Rev. Cell Dev. Biol. 24, 131–157 (2008).

    Article  CAS  PubMed  Google Scholar 

  121. Santoro, R. & Grummt, I. Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription. Mol. Cell 8, 719–725 (2001).

    Article  CAS  PubMed  Google Scholar 

  122. Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease. Nat. Rev. Mol. Cell Biol. 20, 590–607 (2019).

    Article  CAS  PubMed  Google Scholar 

  123. Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010).

    Article  CAS  PubMed  Google Scholar 

  124. Rausch, C. et al. Cytosine base modifications regulate DNA duplex stability and metabolism. Nucleic Acids Res. 49, 12870–12894 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Yao, R. W. et al. Nascent pre-rRNA sorting via phase separation drives the assembly of dense fibrillar components in the human nucleolus. Mol. Cell 76, 767–783.e11 (2019).

    Article  CAS  PubMed  Google Scholar 

  126. Maiser, A. et al. Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus. Sci. Rep. 10, 7462 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. van Sluis, M., van Vuuren, C., Mangan, H. & McStay, B. NORs on human acrocentric chromosome p-arms are active by default and can associate with nucleoli independently of rDNA. Proc. Natl Acad. Sci. USA 117, 10368–10377 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  128. Sanij, E. et al. UBF levels determine the number of active ribosomal RNA genes in mammals. J. Cell Biol. 183, 1259–1274 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Eickbush, T. H. & Eickbush, D. G. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175, 477–485 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Mars, J. C., Sabourin-Felix, M., Tremblay, M. G. & Moss, T. A deconvolution protocol for ChIP-seq reveals analogous enhancer structures on the mouse and human ribosomal RNA genes. G3 (Bethseda) 8, 303–314 (2018).

    Article  CAS  Google Scholar 

  131. Herdman, C. et al. A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription. PLoS Genet. 13, e1006899 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  132. Kireeva, M. L. et al. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol. Cell 9, 541–552 (2002).

    Article  CAS  PubMed  Google Scholar 

  133. Grummt, I. & Pikaard, C. S. Epigenetic silencing of RNA polymerase I transcription. Nat. Rev. Mol. Cell Biol. 4, 641–649 (2003).

    Article  CAS  PubMed  Google Scholar 

  134. Chen, Z. J. & Pikaard, C. S. Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev. 11, 2124–2136 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Srivastava, R., Srivastava, R. & Ahn, S. H. The epigenetic pathways to ribosomal DNA silencing. Microbiol. Mol. Biol. Rev. 80, 545–563 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Santoro, R., Li, J. & Grummt, I. The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat. Genet. 32, 393–396 (2002).

    Article  CAS  PubMed  Google Scholar 

  137. Yang, L. et al. Regulation of SirT1-nucleomethylin binding by rRNA coordinates ribosome biogenesis with nutrient availability. Mol. Cell. Biol. 33, 3835–3848 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Murayama, A. et al. Epigenetic control of rDNA loci in response to intracellular energy status. Cell 133, 627–639 (2008).

    Article  CAS  PubMed  Google Scholar 

  139. Ianni, A., Hoelper, S., Krueger, M., Braun, T. & Bober, E. Sirt7 stabilizes rDNA heterochromatin through recruitment of DNMT1 and Sirt1. Biochem. Biophys. Res. Commun. 492, 434–440 (2017).

    Article  CAS  PubMed  Google Scholar 

  140. Stefanovsky, V. Y. et al. An immediate response of ribosomal transcription to growth factor stimulation in mammals is mediated by ERK phosphorylation of UBF. Mol. Cell 8, 1063–1073 (2001).

    Article  CAS  PubMed  Google Scholar 

  141. James, M. J. & Zomerdijk, J. C. B. M. Phosphatidylinositol 3-kinase and mTOR signaling pathways regulate RNA polymerase I transcription in response to IGF-1 and nutrients. J. Biol. Chem. 279, 8911–8918 (2004).

    Article  CAS  PubMed  Google Scholar 

  142. Xie, W. et al. The chromatin remodeling complex NuRD establishes the poised state of rRNA genes characterized by bivalent histone modifications and altered nucleosome positions. Proc. Natl Acad. Sci. USA 109, 8161–8166 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Ling, T. et al. CHD4/NuRD maintains demethylation state of rDNA promoters through inhibiting the expression of the rDNA methyltransferase recruiter TIP5. Biochem. Biophys. Res. Commun. 437, 101–107 (2013).

    Article  CAS  PubMed  Google Scholar 

  144. Lafontaine, D. L. J., Riback, J. A., Bascetin, R. & Brangwynne, C. P. The nucleolus as a multiphase liquid condensate. Nat. Rev. Mol. Cell Biol. 22, 165–182 (2021).

    Article  CAS  PubMed  Google Scholar 

  145. Kempers-Veenstra, A. E. et al. 3’-end formation of transcripts from the yeast rRNA operon. EMBO J. 5, 2703–2710 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Strauss, S. et al. Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging. Nat. Methods 15, 685–688 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Klinge, S. & Woolford, J. L. Ribosome assembly coming into focus. Nat. Rev. Mol. Cell Biol. 20, 116–131 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Albert, B., Perez-Fernandez, J., Léger-Silvestre, I. & Gadal, O. Regulation of ribosomal RNA production by RNA polymerase I: does elongation come first? Genet. Res. Int. 2012, 1–13 (2012).

    Article  Google Scholar 

  149. Scheer, U. & Benavente, R. Functional and dynamic aspects of the mammalian nucleolus. BioEssays 12, 14–21 (1990).

    Article  CAS  PubMed  Google Scholar 

  150. Mougey, E. B. et al. The terminal balls characteristic of eukaryotic rRNA transcription units in chromatin spreads are rRNA processing complexes. Genes Dev. 7, 1609–1619 (1993).

    Article  CAS  PubMed  Google Scholar 

  151. Floutsakou, I. et al. The shared genomic architecture of human nucleolar organizer regions. Genome Res. 23, 2003–2012 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Van Koningsbruggen, S. et al. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol. Biol. Cell 21, 3735–3748 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  153. Yu, S. & Lemos, B. The long-range interaction map of ribosomal DNA arrays. PLoS Genet. 14, e1007258 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  154. Gupta, S. & Santoro, R. Regulation and roles of the nucleolus in embryonic stem cells: from ribosome biogenesis to genome organization. Stem Cell Rep. 15, 1206–1219 (2020).

    Article  CAS  Google Scholar 

  155. Meshorer, E. & Misteli, T. Chromatin in pluripotent embryonic stem cells and differentiation. Nat. Rev. Mol. Cell Biol. 7, 540–546 (2006).

    Article  CAS  PubMed  Google Scholar 

  156. Casafont, I. et al. The giant fibrillar center: a nucleolar structure enriched in upstream binding factor (UBF) that appears in transcriptionally more active sensory ganglia neurons. J. Struct. Biol. 159, 451–461 (2007).

    Article  CAS  PubMed  Google Scholar 

  157. Lafarga, M., Villegas, J. & Crespo, D. Changes in nucleolar morphology and volume of the supraoptic nucleus neurons during postnatal development of the rat. Dev. Brain Res. 22, 310–313 (1985).

    Article  Google Scholar 

  158. Brangwynne, C. P. et al. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324, 1729–1732 (2009).

    Article  CAS  PubMed  Google Scholar 

  159. Brangwynne, C. P., Mitchison, T. J. & Hyman, A. A. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc. Natl Acad. Sci. USA 108, 4334–4339 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Alberti, S., Gladfelter, A. & Mittag, T. Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell 176, 419–434 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Feric, M. et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686–1697 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Riback, J. A. et al. Composition-dependent thermodynamics of intracellular phase separation. Nature 581, 209–214 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Hnisz, D., Shrinivas, K., Young, R. A., Chakraborty, A. K. & Sharp, P. A. A phase separation model for transcriptional control. Cell 169, 13–23 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Manteiga, J. C. et al. Pol II phosphorylation regulates a switch between transcriptional and splicing condensates. Nature 572, 543 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  165. Boehning, M. et al. RNA polymerase II clustering through carboxy-terminal domain phase separation. Nat. Struct. Mol. Biol. 25, 833–840 (2018).

    Article  CAS  PubMed  Google Scholar 

  166. Lu, H. et al. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Nature 558, 318–323 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Thiry, M. & Lafontaine, D. L. J. Birth of a nucleolus: the evolution of nucleolar compartments. Trends Cell Biol. 15, 194–199 (2005).

    Article  CAS  PubMed  Google Scholar 

  168. Riback, J. A. et al. Viscoelastic RNA entanglement and advective flow underlies nucleolar form and function. bioRxiv https://doi.org/10.1101/2021.12.31.474660 (2022).

    Article  Google Scholar 

  169. Mooser, C. et al. Treacle controls the nucleolar response to rDNA breaks via TOPBP1 recruitment and ATR activation. Nat. Commun. 11, 123 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Ide, S., Imai, R., Ochi, H. & Maeshima, K. Transcriptional suppression of ribosomal DNA with phase separation. Sci. Adv. 6, 1–16 (2020).

    Article  Google Scholar 

  171. Shin, Y. et al. Spatiotemporal control of intracellular phase transitions using light-activated optoDroplets. Cell 168, 159–171.e14 (2017).

    Article  CAS  PubMed  Google Scholar 

  172. Klosin, A. et al. Phase separation provides a mechanism to reduce noise in cells. Sci 367, 464–468 (2020).

    Article  CAS  Google Scholar 

  173. Neurohr, G. E. et al. Deregulation of the G1/S-phase transition is the proximal cause of mortality in old yeast mother cells. Genes Dev. 32, 1075–1084 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Morlot, S. et al. Excessive rDNA transcription drives the disruption in nuclear homeostasis during entry into senescence in budding yeast. Cell Rep. 28, 408–422.e4 (2019).

    Article  CAS  PubMed  Google Scholar 

  175. Crane, M. M. et al. DNA damage checkpoint activation impairs chromatin homeostasis and promotes mitotic catastrophe during aging. Elife 8, e50778 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Ganley, A. R. D., Ide, S., Saka, K. & Kobayashi, T. The effect of replication initiation on gene amplification in the rDNA and its relationship to aging. Mol. Cell 35, 683–693 (2009).

    Article  CAS  PubMed  Google Scholar 

  177. Goto, M., Sasaki, M. & Kobayashi, T. The S-phase cyclin Clb5 promotes rRNA gene (rDNA) stability by maintaining replication initiation efficiency in rDNA. Mol. Cell. Biol. 41, e00324-20 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  178. Hattori, M., Horigome, C., Aspert, T., Charvin, G. & Kobayashi, T. Changed life course upon defective replication of ribosomal RNA genes. Genes Genet. Syst. (In the press).

  179. Pal, S., Postnikoff, S. D., Chavez, M. & Tyler, J. K. Impaired cohesion and homologous recombination during replicative aging in budding yeast. Sci. Adv. 4, eaaq0236 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  180. Ganley, A. R. D. & Kobayashi, T. Ribosomal DNA and cellular senescence: new evidence supporting the connection between rDNA and aging. FEMS Yeast Res. 14, 49–59 (2014).

    Article  CAS  PubMed  Google Scholar 

  181. Xu, B. et al. Ribosomal DNA copy number loss and sequence variation in cancer. PLoS Genet. 13, e1006771 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  182. Hall, A. N., Morton, E. & Queitsch, C. First discovered, long out of sight, finally visible: ribosomal DNA. Trends Genet. 38, 587–597 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Watada, E. et al. Age-dependent ribosomal DNA variations in mice. Mol. Cell. Biol. 40, e00368-20 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  184. D’Aquila, P. et al. Methylation of the ribosomal RNA gene promoter is associated with aging and age-related decline. Aging Cell 16, 966–975 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  185. Wang, M. & Lemos, B. Ribosomal DNA harbors an evolutionarily conserved clock of biological aging. Genome Res. 29, 325–333 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Weaver, K. N. et al. Acrofacial dysostosis, Cincinnati type, a mandibulofacial dysostosis syndrome with limb anomalies, is caused by POLR1A dysfunction. Am. J. Hum. Genet. 96, 765–774 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Thiffault, I. et al. Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III. Nat. Commun. 6, 7623 (2015).

    Article  PubMed  Google Scholar 

  188. Schaefer, E. et al. Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome. Genet. Med. 16, 720–724 (2014).

    Article  CAS  PubMed  Google Scholar 

  189. Dauwerse, J. G. et al. Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nat. Genet. 43, 20–22 (2011).

    Article  CAS  PubMed  Google Scholar 

  190. Sanchez, E. et al. POLR1B and neural crest cell anomalies in Treacher Collins syndrome type 4. Genet. Med. 22, 547–556 (2020).

    Article  PubMed  Google Scholar 

  191. Kara, B. et al. Severe neurodegenerative disease in brothers with homozygous mutation in POLR1A. Eur. J. Hum. Genet. 25, 315–323 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Zhao, D. et al. Structure of the human RNA polymerase I elongation complex. Cell Discov. 7, 97 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Li, L. et al. Structure of human RNA polymerase III elongation complex. Cell Res. 31, (2021).

  194. Wang, Q. et al. Structural insights into transcriptional regulation of human RNA polymerase III. Nat. Struct. Mol. Biol. 28, 220–227 (2021).

    Article  CAS  PubMed  Google Scholar 

  195. Ramsay, E. P. et al. Structure of human RNA polymerase III. Nat. Commun. 11, 6409 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Girbig, M. et al. Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states. Nat. Struct. Mol. Biol. 28, 210–219 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Müller, F. et al. A prebiotically plausible scenario of an RNA–peptide world. Nature 605, 279–284 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  198. Goffová, I. & Fajkus, J. The rDNA loci — intersections of replication, transcription, and repair pathways. Int. J. Mol. Sci. 22, 1302 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  199. Roichman, A. et al. Restoration of energy homeostasis by SIRT6 extends healthy lifespan. Nat. Commun. 12, 3208 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Yoshida, M. et al. Extracellular vesicle-contained eNAMPT delays aging and extends lifespan in mice. Cell Metab. 30, 329–342.e5 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Yoshino, M. et al. Nicotinamide mononucleotide increases muscle insulin sensitivity in prediabetic women. Science 372, 1224–1229 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Ferreira, R., Schneekloth, J. S., Panov, K. I., Hannan, K. M. & Hannan, R. D. Targeting the RNA polymerase I transcription for cancer therapy comes of age. Cells 9, 266 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Haag, J. R. & Pikaard, C. S. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol. 12, 483–492 (2011).

    Article  CAS  PubMed  Google Scholar 

  204. Grimm, C. et al. Structural basis of Poxvirus transcription: vaccinia RNA polymerase complexes. Cell 179, 1537–1550.e19 (2019).

    Article  CAS  PubMed  Google Scholar 

  205. Nogi, Y., Yano, R. & Nomura, M. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I. Proc. Natl Acad. Sci. USA 88, 3962–3966 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Kawauchi, J., Mischo, H., Braglia, P., Rondon, A. & Proudfoot, N. J. Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes Dev. 22, 1082–1092 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Reiter, A. et al. The Reb1-homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J. 31, 3480–3493 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  208. Evers, R., Smid, A., Rudloff, U., Lottspeich, F. & Grummt, I. Different domains of the murine RNA polymerase I-specific termination factor mTTF-I serve distinct functions in transcription termination. EMBO J. 14, 1248–1256 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Wittner, M. et al. Establishment and maintenance of alternative chromatin states at a multicopy gene locus. Cell 145, 543–554 (2011).

    Article  CAS  PubMed  Google Scholar 

  210. Merz, K. et al. Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. Genes Dev. 22, 1190–1204 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. Putnam, C. D., Copenhaver, G. P., Denton, M. L. & Pikaard, C. S. The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA. Mol. Cell. Biol. 14, 6476–6488 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  212. Panov, K. I., Friedrich, J. K., Russell, J. & Zomerdijk, J. C. B. M. UBF activates RNA polymerase I transcription by stimulating promoter escape. EMBO J. 25, 3310–3322 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We apologize to the colleagues whose work could not be cited owing to space constraints. T.K. thanks all the collaborators who work together to study rDNA and to the members of his laboratory. T.K. is supported by JST CREST (grant number JPMJCR19S3), AMED-CREST (JP20gm1110010) and Grants-in-Aid for Scientific Research (17H01443 and 21H04761) from the Japan Society for the Promotion of Science. C.E. thanks A. Griesenbeck and A. Stutz for comments, and all past and present members of the Structural Biochemistry Group within the Regensburg Center for Biochemistry. C.E. acknowledges funding by the German Research Council’s Emmy Noether Programme (DFG grant EN 1204/1-1) and the Collaborative Research Center 960 (Project A8).

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  1. Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan

    Yutaro Hori & Takehiko Kobayashi

  2. Structural Biochemistry Group, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany

    Christoph Engel

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Glossary

Acrofacial dysostosis (Cincinnati type)

A rare hereditary disorder leading to unusual facial development owing to defective development of bones in the jaw and arms.

General transcription factors

Transcription factors that bind to specific promoter DNA sites to activate transcription with the RNA polymerase.

Histone fold domain

A conserved protein fold consisting of ~70 amino acids that form three α-helices; found in many proteins and responsible for the formation of four heterodimers of histone proteins within canonical nucleosomes.

HMG box

A domain found in high mobility group (HMG) proteins. An evolutionarily conserved tertiary fold of ~75 residues that can interact with non-B-from double-stranded DNA in sequence-specific or non-sequence-specific manners or promote protein–protein interactions.

Hypomyelinating leukodystrophy

A rare hereditary disorder with aberrant myelin formation in the central nervous system.

Negative stain electron microscopy

A staining technique to visualize electron microscopy grid-adsorbed macromolecular particles as exclusion spaces in room-temperature electron microscopy.

Progeroid syndromes

A group of progressive genetic disorders that mimic physiological ageing and that are often caused by mutations in DNA repair genes.

Psoralen

A chemical that is intercalated into and covalently binds DNA upon UV exposure. As psoralen cannot be intercalated into nucleosome-rich DNA, it is used to assess DNA accessibility.

Treacher Collins syndrome

A rare hereditary disorder resulting in deformities of the ears, eyes, cheekbones and chin.

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Hori, Y., Engel, C. & Kobayashi, T. Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 24, 414–429 (2023). https://doi.org/10.1038/s41580-022-00573-9

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