Skip to main content

Nucleotide sequence, structural organization and length heterogeneity of ribosomal DNA intergenic spacer in Quercus petraea (Matt.) Liebl. and Q. robur L.

Abstract

18S-5.8S-26S rDNA family comprises tandemly arranged, repeating units separated by an intergenic spacer (IGS) that contains transcription initiation/termination signals and usually repeating elements. In this study, we performed for the first time thorough sequence analysis of rDNA IGS region in two dominant European oaks, Quercus petraea and Q. robur, in order to investigate (1) if IGS sequence composition allows discrimination between these two species, and (2) if there is an rDNA length heterogeneity arising from IGS sequence. Two spacer length variants (slvs), 2 and 4 kb in length, were found in the genomes of both species. Inter-comparison of both slvs revealed no species-specificity in sequence or structural organization. Both slvs could be divided into four subregions; (1) the subrepeat region containing three repeated elements, (2) the AT-rich region containing matrix attachment sites and putative origin of replication, (3) the promoter region containing putative transcription initiation site and (4) the 5′ETS region. In the 4-kb slvs all four subregions are extended, and the subrepeat, AT-rich and promoter regions are duplicated. This is unique compared to other known IGS sequences where the variation in number of subrepeats is responsible for slvs creation. We also propose a possible evolutionary scenario to explain the formation of the subrepeat region in oak IGS. Results obtained in this work add to the previous picture of low-genetic differentiation of the two oaks and provide important data for further analyses of the function of IGS in control of rRNA gene expression.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4a
Fig. 4b
Fig. 5
Fig. 6
Fig. 7
Fig. 8

References

  • Baldridge GD, Dalton MW, Fallon AM (1992) Is higher-order structure conserved in eukaryotic ribosomal DNA intergenic spacers? J Mol Evol 35:514–523

    PubMed  Article  CAS  Google Scholar 

  • Barreneche T, Bahrman N, Kremer A (1996) Two dimensional gel electrophoresis confirms the low level of genetic differentiation between Quercus robur L. and Qurecus petraea (Matt.). Liebl For Genet 3:89–92

    Google Scholar 

  • Bellarosa R, Delre V, Schirone B, Maggini F (1990) Ribosomal RNA genes in Quercus spp. (Fagaceae). Plant Syst Evol 172:127–139

    Article  CAS  Google Scholar 

  • Bellarosa R, Simeone MC, Papini A, Schirone B (2005) Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp. Mol Phylogenet Evol 34:355–370

    PubMed  Article  CAS  Google Scholar 

  • Bobola MS, Smith DE, Klein AS (1992) Five major nuclear ribosomal repeats represent a large and variable fraction of the genomic DNA of Picea rubens and P. mariana. Mol Biol Evol 9:125–137

    PubMed  CAS  Google Scholar 

  • Bodenes C, Joandet S, Laigret F, Kremer A (1997) Detection of genomic region differentiating two closely related oak species Quercus petraea (Matt.) Liebl. and Quercus robur L. Heredity 78:433–444

    Article  CAS  Google Scholar 

  • Borisjuk L, Hemleben V (1992) Nucleotide sequence of potato rDNA intergenic spacer. Plant Mol Biol 21:381–384

    Article  Google Scholar 

  • Borisjuk NV, Davidjuk YM, Kostishin SS, Miroshnichenco GP, Velasco R, Hemleben V, Volkov RA (1997) Structural analysis of rDNA in the genus Nicotiana. Plant Mol Biol 35:655–660

    PubMed  Article  CAS  Google Scholar 

  • Coart E, Lamote V, De Loose M, Van Bockstaele E, Lootens P, Roldan-Ruiz I (2002) AFLP markers demonstrate local genetic differentiation between two indigenous oak species (Quercus robur L. and Quercus petraea (Matt.) Liebl.) in Flemish populations. Theor Appl Genet 105:431–439

    PubMed  Article  CAS  Google Scholar 

  • Coffman FD, He M, Diaz M-L, Cohen S (2006) Multiple initiation sites within the human ribosomal RNA gene. Cell Cycle 5:1223–1233

    PubMed  CAS  Google Scholar 

  • Cordesse F, Cooke R, Tremousaygue D, Grellet F, Delseny M (1993) Fine structure and evolution of the rDNA intergenic spacer in rice and other cereals. J Mol Evol 36:369–379

    PubMed  Article  CAS  Google Scholar 

  • Crothers DM, Haran TE, Nadeau JG (1990) Intrinsically bent DNA. J Biol Chem 265:7093–7096

    PubMed  CAS  Google Scholar 

  • Cullis CA, Creissen GP, Gorman SW, Tiasdale RD (1988) The 25S, 18S and 5S ribosomal RNA genes from Pinus radiata D.Don. In: Cheliak WM, Yappa AA (eds) Molecular genetics of forest trees. Canadian Forest service, Petawawa National forest Institute, pp 34–40

  • Dadejova M, Lim KY, Souckova-Skalicka K, Matyasek R, Grandbastien MA, Leitch A, Kovarik A (2007) Transcription activity of rRNA genes correlates with a tendency towards intergenomic homogenization in Nicotiana allotetraploids. New Phytol 174:658–668

    PubMed  Article  CAS  Google Scholar 

  • Delcasso-Tremousaygue D, Grellet F, Panabieres F, Ananiev ED, Delseny M (1988) Structural and transcriptional characterization of the external spacer of a ribosomal RNA nuclear gene from a higher plant. Eur J Biochem 172:767–776

    PubMed  Article  CAS  Google Scholar 

  • Doelling JH, Gaudino GJ, Pikaard CS (1993) Functional analysis of Arabidopsis thaliana rRNA gene and spacer promoters in vivo and by transient expression. Proc Natl Acad Sci USA 90:7528–7532

    PubMed  Article  CAS  Google Scholar 

  • Fan H, Yakura K, Miyanishi M, Sugita M, Sugiura M (1995) In vitro transcription of plant RNA polymerase I-dependent rRNA genes is species-specific. Plant J 8:295–298

    PubMed  Article  CAS  Google Scholar 

  • Fernandez M, Polanco C, Ruiz ML, de la Vega PM (2000) A comparative study of the structure of the rDNA intergenic spacer of Lens culinaris Medik., and other legume species. Genome 43:597–603

    PubMed  Article  CAS  Google Scholar 

  • Ghoshal K, Majumder S, Datta J, Motiwala T, Bai S, Sharma SM, Frankel W, Jacob ST (2004) Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression. J Biol Chem 279:6783–6793

    PubMed  Article  CAS  Google Scholar 

  • Gonzalez IL, Sylvester JE (1995) Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer. Genomics 27:320–328

    PubMed  Article  CAS  Google Scholar 

  • Grimaldi G, Fiorentini P, Di Nocera PP (1990) Spacer promoters are orientation-dependent activators of pre-rRNA transcription in Drosophila melanogaster. Mol Cell Biol 10:4667–4677

    PubMed  CAS  Google Scholar 

  • Grozdanov P, Georgiev O, Karagyozov L (2003) Complete sequence of the 45-kb mouse ribosomal DNA repeat: analysis of the intergenic spacer. Genomics 82:637–643

    PubMed  Article  CAS  Google Scholar 

  • Gruendler P, Unfried I, Pascher K, Schweizer D (1991) rDNA intergenic region from Arabidopsis thaliana: structural analysis, intraspecific variation and functional implication. J Mol Biol 221:1209–1222

    PubMed  Article  CAS  Google Scholar 

  • Hernandez P, Martin-Parras L, Martinez-Robles ML, Schvartzman JB (1993) Conserved features in the mode of replication of eucaryotic ribosomal RNA genes. EMBO J 12:1475–1485

    PubMed  CAS  Google Scholar 

  • Huang Y, Kowalski D (2003) WEB-THERMODYN: sequence analysis software for profiling DNA helical stability. Nucleic Acids Res 31:3819–3821

    PubMed  Article  CAS  Google Scholar 

  • Kelly RJ, Siegel A (1989) The Cucurbita maxima ribosomal DNA intergenic spacer has a complex structure. Gene 80:239–248

    PubMed  Article  CAS  Google Scholar 

  • Kuhn A, Deppert U, Grummt I (1990) A 140-base-pair repetitive sequence element in the mouse rRNA gene spacer enhances transcription by RNA polymerase I in a cell-free system. Proc Natl Acad Sci USA 87:7527–7531

    PubMed  Article  CAS  Google Scholar 

  • Kuhn A, Voit R, Stefanovsky V, Evers R, Bianchi M, Grummt I (1994) Functional differences between the two splice variants of the nucleolar transcription factor UBF: the second HMG box determines specificity of DNA binding and transcriptional activity. EMBO J 13:416–424

    PubMed  CAS  Google Scholar 

  • Mayer C, Schmitz KM, Li J, Grummt I, Santoro R (2006) Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell 22:351–361

    PubMed  Article  CAS  Google Scholar 

  • McMullen MD, Hunter B, Phillips RL, Rubenstein I (1986) The structure of the maize ribosomal DNA spacer region. Nucleic Acids Res 14:4953–4968

    PubMed  Article  CAS  Google Scholar 

  • Miyano M, Kawashima T, Ohyama T (2001) A common feature shared by bent DNA structures locating in the eukaryotic promoter region. Mol Biol Rep 28:53–61

    PubMed  Article  CAS  Google Scholar 

  • Moss T, Stefanovsky VY (1995) Promotion and regulation of ribosomal transcription in eukaryotes by RNA polymerase I. Nucleic Acids Res Mol Biol 50:25–66

    Article  CAS  Google Scholar 

  • Muir G, Fleming CC, Schlotterer C (2000) Species status of hybridizing oaks. Nature 405:1016

    PubMed  Article  CAS  Google Scholar 

  • Perry KL, Palukaitis P (1990) Transcription of tomato ribosomal DNA and the organization of the intergenic spacer. Mol Gen Genet 221:102–112

    Article  CAS  Google Scholar 

  • Pikaard CS (1994) Ribosomal gene promoter domains can function as artificial enhancers of RNA polymerase I transcription, supporting a promoter origin for natural enhancers in Xenopus. Proc Natl Acad Sci USA 91:464–468

    PubMed  Article  CAS  Google Scholar 

  • Preuss S, Pikaard CS (2007) rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch. Biochim Biophys Acta 1769:383–392

    PubMed  CAS  Google Scholar 

  • Rathgeber J, Capesius I (1990) Nucleotide sequence of the intergenic spacer and the 18S ribosomal RNA gene from mustard (Sinapis alba). Nucleic Acids Res 18:1288

    PubMed  Article  CAS  Google Scholar 

  • Reed KM, Hackett JD, Phillips RB (2000) Comparative analysis of intra-individual and inter-species DNA sequence variation in salmonid ribosomal DNA cistrons. Gene 249:115–125

    PubMed  Article  CAS  Google Scholar 

  • Reed KM, Phillips RB (2000) Structure and organisation of the rDNA intergenic spacer in lake trout (Salvelinus namaycush). Chrom Res 8:5–16

    PubMed  Article  CAS  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    PubMed  Article  CAS  Google Scholar 

  • Samuel R, Pinsker W, Ehrendorfer F (1995) Electrophoretic analysis of genetic variation within and between populations of Quercus cerris, Q. pubescens, Q. petraea and Q. robur (Fagaceae) from eastern Austria. Bot Acta 108:290–299

    CAS  Google Scholar 

  • Schnare MN, Collings JC, Spencer DF, Gray MW (2000) The 28S-18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences. Length heterogeneity, putative processing sites and potential interactions between U3 and small nucleolar RNA and the ribosomal precursor. Nucleic Acids Res 28:3452–3461

    PubMed  Article  CAS  Google Scholar 

  • Suzuki A, Tanifuji S, Komeda Y, Kato A (1996) Structural and functional characterization of the intergenic spacer of the rDNA in Daucus carota. Plant Cell Physiol 37:233–238

    PubMed  CAS  Google Scholar 

  • Suzuki H, Miyashita N, Moriwaki K, Kominami R, Muramatsu M, Kanehisa T, Bonhomme F, Petras ML, Ze-Chang Y, De-Yuan L (1986) Evolutionary implication of heterogeneity of the nontranscribed spacer region of ribosomal DNA repeating units in various subspecies of Mus musculus. Mol Biol Evol 3:126–137

    PubMed  CAS  Google Scholar 

  • Torres-Ruiz RA, Hemleben V (1994) Pattern and degree of methylation in ribosomal RNA genes of Cucurbita pepo L. Plant Mol Biol 26:1167–1179

    PubMed  Article  CAS  Google Scholar 

  • Whittemore AT, Schaal BA (1991) Interspecific gene flow in sympatric oaks. Proc Natl Acad Sci USA 88:2540–2544

    PubMed  Article  CAS  Google Scholar 

  • Zanetto A, Roussel G, Kremer A (1994) Geographic variation of inter-specific differentiation between Quercus robur L. and Quercus petraea (Matt.) Liebl. For Genet 99:111–123

    Google Scholar 

  • Zemach A, Grafi G (2003) Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J 34:565–572

    PubMed  Article  CAS  Google Scholar 

  • Zoldos V, Papes D, Brown SC, Panaud O, Siljak-Yakovlev S (1998) Genome size and base composition of seven Quercus species: inter- and intra-population variation. Genome 41:162–168

    Article  CAS  Google Scholar 

  • Zoldos V, Papes D, Cerbah M, Panaud O, Besendorfer V, Siljak-Yakovlev S (1999) Molecular-cytogenetic studies of ribosomal genes and heterochromatin reveal conserved genome organization among 11 Quercus species. Theor Appl Genet 99:969–977

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was funded by the Ministry of Science, Education and Sport of the Republic of Croatia, grants 119-1191196-1224 and 119-1191196-1225. We thank prof. Ž. Borzan for providing biological material.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Vlatka Zoldoš.

Additional information

Communicated by R. Hagemann.

N. Bauer and T. Horvat contributed equally to the manuscript.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Tables and Figures (PDF 276 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Bauer, N., Horvat, T., Biruš, I. et al. Nucleotide sequence, structural organization and length heterogeneity of ribosomal DNA intergenic spacer in Quercus petraea (Matt.) Liebl. and Q. robur L.. Mol Genet Genomics 281, 207–221 (2009). https://doi.org/10.1007/s00438-008-0404-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-008-0404-8

Keywords

  • IGS
  • Spacer length variants
  • rRNA genes
  • Repetitive elements
  • Quercus petraea
  • Q. robur