Abstract
The rRNA genes of mouse and human encode the three major RNAs of the ribosome and as such are essential for growth and development. These genes are present in high copy numbers and arranged as direct repeats at the Nucleolar Organizer Regions on multiple chromosomes. Not all the rRNA genes are transcriptionally active, but the molecular mechanisms that determine activity are complex and still poorly understood. Recent studies applying a novel Deconvolution Chromatin Immunoprecipitation (DChIP-Seq) technique in conjunction with conditional gene inactivation provide new insights into the structure of the active rRNA genes and question previous assumptions on the role of chromatin and histone modifications. We suggest an alternative model for the active rRNA gene chromatin and discuss how this structure is determined and maintained.
Similar content being viewed by others
Abbreviations
- RPI:
-
RNA polymerase I, POLR1, POL1
- RPII:
-
RNA polymerase II, POLR2, POL2
- RRN3:
-
RPI associated factor
- rRNA:
-
Ribosomal RNA
- rDNA:
-
Ribosomal DNA
- SL1:
-
RNA polymerase 1-specific TBP-TAF complex
- UBF:
-
Upstream binding factor, UBTF
References
Bazett-Jones DP, Leblanc B, Herfort M, Moss T (1994) Short-range DNA looping by the Xenopus HMG-box transcription factor, xUBF. Science 264:1134–1137
Billon P, Cote J (2012) Precise deposition of histone H2A.Z in chromatin for genome expression and maintenance. Biochim Biophys Acta 1819:290–302. https://doi.org/10.1016/j.bbagrm.2011.10.004
Bilodeau S, Young RA (2011) ChIP-Seq data for histone marks in mouse embryonic fibroblasts. (data accessible at NCBI GEO database, accession GSE26657)
Birch JL, Zomerdijk JC (2008) Structure and function of ribosomal RNA gene chromatin. Biochem Soc Trans 36:619–624. https://doi.org/10.1042/BST0360619
Bruce K, Myers FA, Mantouvalou E, Lefevre P, Greaves I, Bonifer C, Tremethick DJ, Thorne AW, Crane-Robinson C (2005) The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken. Nucleic Acids Res 33:5633–5639. https://doi.org/10.1093/nar/gki874
Brunelle M, Nordell Markovits A, Rodrigue S, Lupien M, Jacques P-É, Gévry N (2015) The histone variant H2AZ is an important regulator of enhancer activity. Nucleic Acids Res 43:9742–9756. https://doi.org/10.1093/nar/gkv825
Bulut-Karslioglu A, de la Rosa-Velázquez IA, Ramirez F, Barenboim M, Onishi-Seebacher M, Arand J, Galán C, Winter GE, Engist B, Gerle B, O’Sullivan RJ, Martens JHA, Walter J, Manke T, Lachner M, Jenuwein T (2014) Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells. Mol Cell 55:277–290. https://doi.org/10.1016/j.molcel.2014.05.029
Conconi A, Widmer RM, Koller T, Sogo JM (1989) Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57:753–761
Dammann R, Lucchini R, Koller T, Sogo JM (1993) Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res 21:2331–2338
De Winter RF, Moss T (1987) A complex array of sequences enhances ribosomal transcription in Xenopus laevis. J Mol Biol 196:813–827
Dev VG, Tantravahi R, Miller DA, Miller OJ (1977) Nucleolus organizers in Mus musculus subspecies and in the RAG mouse cell line. Genetics 86:389–398
Evers R, Grummt I (1995) Molecular coevolution of mammalian ribosomal gene terminator sequences and the transcription termination factor TTF-I. Proc Natl Acad Sci U S A 92:5827–5831
French SL, Osheim YN, Cioci F, Nomura M, Beyer AL (2003) 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
Gagnon-Kugler T, Langlois F, Stefanovsky V, Lessard F, Moss T (2009) Loss of human ribosomal gene CpG methylation enhances cryptic RNA polymerase II transcription and disrupts ribosomal RNA processing. Mol Cell 35:414–425. https://doi.org/10.1016/j.molcel.2009.07.008
Griesenbeck J, Tschochner H, Grohmann D (2017) Structure and function of RNA polymerases and the transcription machineries. Subcell Biochem 83:225–270. https://doi.org/10.1007/978-3-319-46503-6_9
Grummt I (2003) Life on a planet of its own: regulation of RNA polymerase I transcription in the nucleolus. Genes Dev 17:1691–1702
Grummt I, Pikaard CS (2003) Epigenetic silencing of RNA polymerase I transcription. Nat Rev Mol Cell Biol 4:641–649
Hamdane N, Stefanovsky VY, Tremblay MG, Németh A, Paquet E, Lessard F, Sanij E, Hannan R, Moss T (2014) Conditional inactivation of upstream binding factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body. PLoS Genet 10:e1004505. https://doi.org/10.1371/journal.pgen.1004505
Hamperl S, Wittner M, Babl V, Perez-Fernandez J, Tschochner H, Griesenbeck J (2013) Chromatin states at ribosomal DNA loci. Biochim Biophys Acta. https://doi.org/10.1016/j.bbagrm.2012.12.007
Heliot L, Mongelard F, Klein C, O'Donohue MF, Chassery JM, Robert-Nicoud M, Usson Y (2000) Nonrandom distribution of metaphase AgNOR staining patterns on human acrocentric chromosomes. J Histochem Cytochem 48:13–20
Henderson AS, Warburton D, Atwood KC (1972) Location of ribosomal DNA in the human chromosome complement. Proc Natl Acad Sci U S A 69:3394–3398
Henikoff S (2000) Heterochromatin function in complex genomes. Biochim Biophys Acta 1470:O1–O8
Herdman C, Mars JC, Stefanovsky VY, Tremblay MG, Sabourin-Felix M, Lindsay H, Robinson MD, Moss T (2017) 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. https://doi.org/10.1371/journal.pgen.1006899
Kauzlaric A, Ecco G, Cassano M, Duc J, Imbeault M, Trono D (2017) The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units. PLoS One 12:e0173746. https://doi.org/10.1371/journal.pone.0173746
Kurihara Y, Suh DS, Suzuki H, Moriwaki K (1994) Chromosomal locations of Ag-NORs and clusters of ribosomal DNA in laboratory strains of mice. Mamm Genome 5:225–228
Labhart P, Reeder RH (1984) Enhancer-like properties of the 60/81 bp elements in the ribosomal gene spacer of Xenopus laevis. Cell 37:285–289
Längst G, Becker PB, Grummt I (1998) TTF-I determines the chromatin architecture of the active rDNA promoter. EMBO J 17:3135–3145
Li J, Langst G, Grummt I (2006) NoRC-dependent nucleosome positioning silences rRNA genes. EMBO J 25:5735–5741
Mais C, Wright JE, Prieto JL, Raggett SL, McStay B (2005) UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery. Genes Dev 19:50–64
Marques M, Laflamme L, Gervais AL, Gaudreau L (2010) Reconciling the positive and negative roles of histone H2A.Z in gene transcription. Epigenetics 5:267–272
Mars JC, Sabourin-Felix M, Tremblay MG, Moss T (2018) A deconvolution protocol for chip-seq reveals analogous enhancer structures on the mouse and human ribosomal RNA genes. G3 (Bethesda) 8:303–314. https://doi.org/10.1534/g3.117.300225
Merkl P, Perez-Fernandez J, Pilsl M, Reiter A, Williams L, Gerber J, Bohm M, Deutzmann R, Griesenbeck J, Milkereit P, Tschochner H (2014) Binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Mol Cell Biol 34:3817–3827. https://doi.org/10.1128/mcb.00395-14
Merz K, Hondele M, Goetze H, Gmelch K, Stoeckl U, Griesenbeck J (2008) 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. https://doi.org/10.1101/gad.466908
Moss T (1983) A transcriptional function for the repetitive ribosomal spacer in Xenopus laevis. Nature 302:223–228
Moss T, Langlois F, Gagnon-Kugler T, Stefanovsky V (2007) A housekeeper with power of attorney: the rRNA genes in ribosome biogenesis. Cell Mol Life Sci 64:29–49
Nemeth A, Langst G (2008) Chromatin organization of active ribosomal RNA genes. Epigenetics 3:243–245
Nemeth A, Guibert S, Tiwari VK, Ohlsson R, Langst G (2008) Epigenetic regulation of TTF-I-mediated promoter-terminator interactions of rRNA genes. Embo J 27:1255–1265. https://doi.org/10.1038/emboj.2008.57
Nishibuchi G, Dejardin J (2017) The molecular basis of the organization of repetitive DNA-containing constitutive heterochromatin in mammals. Chromosom Res 25:77–87. https://doi.org/10.1007/s10577-016-9547-3
Ong CT, Corces VG (2014) CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 15:234–246. https://doi.org/10.1038/nrg3663
Pelletier G, Stefanovsky VY, Faubladier M, Hirschler-Laszkiewicz I, Savard J, Rothblum LI, Côté J, Moss T (2000) Competitive recruitment of CBP and Rb-HDAC regulates UBF acetylation and ribosomal transcription. Mol Cell 6:1059–1066
Pikaard CS, Pape LK, Henderson SL, Ryan K, Paalman MH, Lopata MA, Reeder RH, Sollner-Webb B (1990) Enhancers for RNA polymerase I in mouse ribosomal DNA. Mol Cell Biol 10:4816–4825
Ranjan A, Mizuguchi G, FitzGerald PC, Wei D, Wang F, Huang Y, Luk E, Woodcock CL, Wu C (2013) Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement. Cell 154:1232–1245. https://doi.org/10.1016/j.cell.2013.08.005
Reiter A, Hamperl S, Seitz H, Merkl P, Perez-Fernandez J, Williams L, Gerber J, Németh A, Léger I, Gadal O, Milkereit P, Griesenbeck J, Tschochner H (2012) The Reb1-homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J 31:3480–3493. https://doi.org/10.1038/emboj.2012.185
Roussel P, Andre C, Comai L, Hernandez-Verdun D (1996) The rDNA transcription machinery is assembled during mitosis in active NORs and absent in inactive NORs. J Cell Biol 133:235–246
Rowe LB, Janaswami PM, Barter ME, Birkenmeier EH (1996) Genetic mapping of 18S ribosomal RNA-related loci to mouse chromosomes 5, 6, 9, 12, 17, 18, 19, and X. Mamm Genome 7:886–889
Santoro R, Grummt I (2001) Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription. Mol Cell 8:719–725
Santoro R, Li J, Grummt I (2002) The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat Genet 32:393–396
Savic N et al (2014) lncRNA maturation to initiate heterochromatin formation in the nucleolus is required for exit from pluripotency in ESCs. Cell Stem Cell 15:720–734. https://doi.org/10.1016/j.stem.2014.10.005
Schmickel RD (1973) Quantitation of human ribosomal DNA: hybridization of human DNA with ribosomal RNA for quantitation and fractionation. Pediatr Res 7:5–12
Schmitz KM, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24:2264–2269. https://doi.org/10.1101/gad.590910
Shen M, Zhou T, Xie W, Ling T, Zhu Q, Zong L, Lyu G, Gao Q, Zhang F, Tao W (2013) The chromatin remodeling factor CSB recruits histone acetyltransferase PCAF to rRNA gene promoters in active state for transcription initiation. PLoS One 8:e62668. https://doi.org/10.1371/journal.pone.0062668
Skibbens RV (2015) Cell biology: cohesin rings leave loose ends. Curr Biol 25:R108–R110. https://doi.org/10.1016/j.cub.2014.12.015
Smirnov E et al (2006) NORs and their transcription competence during the cell cycle. Folia Biol (Praha) 52:59–70
Stancheva I, Lucchini R, Koller T, Sogo JM (1997) Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking. Nucleic Acids Res 25:1727–1735
Stefanovsky VY, Moss T (2006) Regulation of rRNA synthesis in human and mouse cells is not determined by changes in active gene count. Cell Cycle 5:735–739
Stefanovsky VY, Bazett-Jones DP, Pelletier G, Moss T (1996) The DNA supercoiling architecture induced by the transcription factor xUBF requires three of its five HMG-boxes. Nucleic Acids Res 24:3208–3215
Stefanovsky VY, Pelletier G, Bazett-Jones DP, Crane-Robinson C, Moss T (2001) DNA looping in the RNA polymerase I enhancesome is the result of non-cooperative in-phase bending by two UBF molecules. Nucleic Acids Res 29:3241–3247
Stefanovsky V, Langlois F, Gagnon-Kugler T, Rothblum LI, Moss T (2006) Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling. Mol Cell 21:629–639. https://doi.org/10.1016/j.molcel.2006.01.023
van de Nobelen S, Rosa-Garrido M, Leers J, Heath H, Soochit W, Joosen L, Jonkers I, Demmers J, van der Reijden M, Torrano V, Grosveld F, Delgado MD, Renkawitz R, Galjart N, Sleutels F (2010) CTCF regulates the local epigenetic state of ribosomal DNA repeats. Epigenetics Chromatin 3:19. https://doi.org/10.1186/1756-8935-3-19
Vintermist A, Bohm S, Sadeghifar F, Louvet E, Mansen A, Percipalle P, Ostlund Farrants AK (2011) The chromatin remodelling complex B-WICH changes the chromatin structure and recruits histone acetyl-transferases to active rRNA genes. PLoS One 6:e19184. https://doi.org/10.1371/journal.pone.0019184
Wittner M, Hamperl S, Stockl U, Seufert W, Tschochner H, Milkereit P, Griesenbeck J (2011) Establishment and maintenance of alternative chromatin states at a multicopy gene locus. Cell 145:543–554. https://doi.org/10.1016/j.cell.2011.03.051
Xie W, Ling T, Zhou Y, Feng W, Zhu Q, Stunnenberg HG, Grummt I, Tao W (2012) 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 U S A 109:8161–8166. https://doi.org/10.1073/pnas.1201262109
Yu F, Shen X, Fan L, Yu Z (2015) Analysis of histone modifications at human ribosomal DNA in liver cancer cell. Sci Rep 5:18100. https://doi.org/10.1038/srep18100
Zentner GE, Saiakhova A, Manaenkov P, Adams MD, Scacheri PC (2011) Integrative genomic analysis of human ribosomal DNA. Nucleic Acids Res 39:4949–4960. https://doi.org/10.1093/nar/gkq1326
Zentner GE, Balow SA, Scacheri PC (2014) Genomic characterization of the mouse ribosomal DNA locus. G3 (Bethesda) 4:243–254. https://doi.org/10.1534/g3.113.009290
Zhao Z, Dammert MA, Hoppe S, Bierhoff H, Grummt I (2016) Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning. Nucleic Acids Res 44:8144–8152. https://doi.org/10.1093/nar/gkw496
Zillner K, Komatsu J, Filarsky K, Kalepu R, Bensimon A, Nemeth A (2015) Active human nucleolar organizer regions are interspersed with inactive rDNA repeats in normal and tumor cells. Epigenomics 7:363–378. https://doi.org/10.2217/epi.14.93
Author statement
TM conceived the study and wrote the manuscript, J-CM and MGT performed experimental research, and MS-F analyzed the data from ChIP-Seq. All authors read and approved the manuscript.
Funding
This work was funded by operating grants from the Canadian Institutes of Health Research (CIHR, MOP12205/PJT153266) and the National Science and Engineering Council (NSERC) of Canada. The Research Centre of the Québec University Hospital Centre (CHU de Québec) is supported by the Fonds de Recherche du Québec—Santé (FRQS).
Author information
Authors and Affiliations
Corresponding author
Additional information
Responsible Editor: Jennifer Gerton and Lev Porokhovnik
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Moss, T., Mars, JC., Tremblay, M.G. et al. The chromatin landscape of the ribosomal RNA genes in mouse and human. Chromosome Res 27, 31–40 (2019). https://doi.org/10.1007/s10577-018-09603-9
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10577-018-09603-9