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RNA, genes, genomes and chromosomes: repetitive DNA sequences in plants

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Chromosomes Today

Abstract

In reviewing the nature and evolution of key repetitive DNA sequences in plants, one can start by considering the most evolutionarily ancient of nucleic acid sequences, at the start of the evolutionary process of modern organisms. Work by several groups since the late 1980s has shown that many features of “life” existed in a world where RNA was a key molecule, and this evolved to the present DNA-based living world. This “RNA world” included RNA-catalyzed reactions, making and breaking chemical bonds, transferring energy between different molecular structures, and self-replication mechanisms. Auto-catalytic RNA sequences (ribozymes) have been known since the 1980s. Gesteland and Atkins Ill have pointed out the enormous richness of apparent “relics” from the RNA world that have been discovered in present day organisms.

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References

  1. Gesteland RF, Atkins JF (1993)The RNA World.Cold Spring Harbor Press, New York

    Google Scholar 

  2. Nitta I, Kamada Y, Noda H, Ueda T, Watanabe K (1998) Reconstitution of peptide bond formation withEscherichia coli23S ribosomal RNA domains.Science281: 666–669

    Article  CAS  PubMed  Google Scholar 

  3. Allen TA (1999)Genomes.Bios, Oxford

    Google Scholar 

  4. Schwarzacher T, Heslop-Harrison JS (2000) Practical in situ hybridization. Bios, Oxford 203 + XII pp

    Google Scholar 

  5. Osuji JO, Crouch J, Harrison G, Heslop-Harrison JS (1998) Molecular cytogenetics ofMusaspecies, cultivars and hybrids: location of 18S-5.8S–25S and 5S rDNA and telomere-like sequences.Ann Bot82: 243–248

    Article  CAS  Google Scholar 

  6. Leitch IJ, Heslop-Harrison JS (1992) Physical mapping of the 18S-5.8S–26S rRNA genes in barley byin situhybridization.Genome35: 1013–1018

    Article  CAS  Google Scholar 

  7. Pedersen C, Rasmussen SK, Linde-Laursen I (1996) Genome and chromosome identification in cultivated barley and related species of the Triticeae(Poaceae)byin situhybridization with the GAA-satellite sequence.Genome39: 93–104

    Article  CAS  PubMed  Google Scholar 

  8. Castilho A, Heslop-Harrison JS (1995) Physical mapping of 5S and 18S–25S rDNA and repetitive DNA sequences inAegilops umbellulata. Genome38: 91–96

    Article  CAS  Google Scholar 

  9. Taketa S, Harrison G, Heslop-Harrison JS (1999) Comparative physical mapping of the 5S and 18S–25S rDNA in nine wildHordeumspecies and cytotypes.TheorAppl Genet98: 1–9

    Article  CAS  Google Scholar 

  10. Dubcovsky J, Dvofák J (1995) Ribosomal RNA multigene loci: Nomads of the triticeae genomes.Genetics140: 1367–1377

    CAS  PubMed  Google Scholar 

  11. Castilho A, Miller TE, Heslop-Harrison JS (1997) Analysis of a set of homologous group 1 wheatAegilops umbellulatarecombinant chromosome lines using genetic markers.TheorAppl Genet94: 293–297

    Article  CAS  Google Scholar 

  12. Leitch IJ, Heslop-Harrison JS (1993) Physical mapping of four sites of 5S rDNA sequences and one site of the alpha-amylase-2 gene in barley(Hordeum vulgare). Genome36: 517–523

    Article  CAS  PubMed  Google Scholar 

  13. Liu L, Saunders K, Thomas C, Davies JW, Stanley J (1999) Bean yellow dwarf virus repA but not rep binds to maize retinoblastoma protein and the virus tolerates mutations in consensus binding motif.Virology256: 270–279

    Article  CAS  PubMed  Google Scholar 

  14. Smit AFA (1996) The origin of interspersed repeats in the human genome.Curr Opin Genet Develop6: 743–748

    Article  CAS  Google Scholar 

  15. Kumar A (1998) The evolution of plant retroviruses: moving to green pastures.Trends Plant Sci3: 371–374

    Article  Google Scholar 

  16. Hull R, Covey SN (1996) Retroelements: propagation and adaptation.Virus Genes 11:105–118

    Article  Google Scholar 

  17. Harper G, Osuji JO, Heslop-Harrison JS, Hull R (1999) Integration of banana streak badnavirus into theMusagenome: molecular and cytogenetic evidence.Virology255: 207–213

    Article  CAS  PubMed  Google Scholar 

  18. Robertson HM, Ellington AD (1998) How to make a nucleotide.Nature395: 223–225

    Article  CAS  PubMed  Google Scholar 

  19. Foiani M, Luccini G, Plevani P (1997) The DNA polymerase-alpha-primase complex couples DNA replication, cell-cycle progression and DNA-damage response.Trends Biochem Sci22: 424–427

    Article  CAS  PubMed  Google Scholar 

  20. San Miguel P, Tikhonov A, Jin Y-K, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z et al (1996) Nested retrotransposons in the intergenic regions of the maize genome.Science274: 737–738

    Article  Google Scholar 

  21. Pearce SR, Harrison G, Wilkinson M, Li D, Heslop-Harrison JS, Flavell AJ, Kumar A 1995. TheTyl -copiagroup retrotransposons inViciaspecies: copy number, sequence heterogeneity and chromosomal localisation.Mol Gen Genet250: 305–315

    Google Scholar 

  22. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RI, Gabriel A, Swergold GD, Kazazian J (1997) Many human Ll elements are capable of retrotransposition.Nat Genet16: 37–43

    Article  CAS  PubMed  Google Scholar 

  23. Leeton PRJ, Smyth DR (1993) An abundant LINE-like element amplified in the genome ofGillum speciosum. Mol Gen Genet237: 97–104

    CAS  Google Scholar 

  24. Goubely C, Arnaud P, Tatout C, Harrison G, Heslop-Harrison JS, Deragon J-M (1999) S1 SINE retroelements are methylated at symmetrical and non-symmetrical positions inBrassica napus:identification of a preffered target site for asymmetrical methylation.Plant Mol Biol39: 243–255

    Article  CAS  PubMed  Google Scholar 

  25. Brandes A, Heslop-Harrison JS, Kamm A, Kubis S, Doudrick RL, Schmidt T (1997) Comparative analysis of the chromosomal and genomic organization ofTyl-copia-likeretrotransposons in pteridophytes, gymnosperms and angiosperms.Plant Mol Biol33: 11–21

    Article  CAS  PubMed  Google Scholar 

  26. Heslop-Harrison JS, Brandes A, Taketa S, Schmidt T, Vershinin AV, Alkhimova EG, Kamm A, Doudrick RL, Schwarzacher T, Katsiotis A et al (1997) The chromosomal distributions of Tylcopiagroup retrotransposable elements in higher plants and their implications for genome evolution.Genetica100: 197–204

    Article  CAS  PubMed  Google Scholar 

  27. Bureau TE, Ronald PC, Wessler SR (1996) A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genomes.Proc Natl Acad Sci USA93: 8524–8529

    Article  CAS  PubMed  Google Scholar 

  28. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Tyl-copia group retro-transposons are ubiquitous and heterogeneous in higher plants.Nucl Acid Res20: 3639–3644

    Article  CAS  Google Scholar 

  29. Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice.Mol Gen Genet233: 209–216

    Article  CAS  PubMed  Google Scholar 

  30. Katsiotis A, Schmidt T, Heslop-Harrison.15 (1996) Chromosomal and genomic organization of Tyl-copia-like retrotransposon sequences in the genusAvena. Genome39: 410–417

    CAS  Google Scholar 

  31. Leggett JM, Markhand GS (1995) The genomic structure ofAvenarevealed by GISH. In: PE Brandham, MD Bennett (eds):Kew Chromosome Conference IVUK, HMSO, 133–139

    Google Scholar 

  32. Katsiotis A, Hagidimitriou M, Heslop-Harrison JS (1997) The close relationship between the A and B genomes inAvenaL. determined by molecular cytogenetic analysis of total genomic, tandemly and dispersed repetitive DNA sequences.Ann Bot79: 103–109

    Article  CAS  Google Scholar 

  33. Pearce SR, Harrison G, Heslop-Harrison JS, Flavell AJ, Kumar A (1997) Characterisation, genomic organisation of Ty1-copia group retrotransposons in rye(Secale cereale). Genome40: 617–625

    Article  CAS  PubMed  Google Scholar 

  34. Wessler SR, Bureau TE, White SE (1995) LTR-retrotransposons and MITEs: important players in the evolution of plant genomes.Curr Opin Genet Develop5: 814–821

    Article  CAS  Google Scholar 

  35. Moran JV, DeBerardinis RJ, Kasasian HH (1999) Exon reshuffling by L1 retrotransposition.Science283: 1530–1534

    Article  Google Scholar 

  36. Schaechter M, von Freiesleben U (1993) The equivalent of mitosis in bacteria. In: JS HeslopHarrison, RB Flavell (eds):The Chromosome.Bios, Oxford, 61–73

    Google Scholar 

  37. Sherratt DJ, Blakely G, Burke M, Colloms S, Leslie N, McCulloch R, May G, Roberts J (1993) Site-specific recombination and the partition of bacterial chromosomes. In: JS Heslop-Harrison, RB Flavell (eds):The Chromosome.Bios, Oxford, 25–41

    Google Scholar 

  38. Saitoh S, Takahashi K, Yanagida M (1997) Mis6, a fission yeast inner centromere protein, acts during G1 /S and forms specialized chromatin required for equal segregation.Cell90: 131–143

    Article  CAS  PubMed  Google Scholar 

  39. Uzawa S, Yanagida M (1992) Visualization of centromeric and nucleolar DNA in fission yeast by fluorescencein situhybridization.J Cell Sci101: 267–275

    PubMed  Google Scholar 

  40. Hegemann JH, Fleig UN (1993) The centromere of budding yeast.Bioessays15: 451–460

    Article  CAS  PubMed  Google Scholar 

  41. Pluta AF, Cooke CA, Earnshaw WC (1990) Structure of the human centromere at metaphase.Trends Biochem Sci15: 181–185

    Article  CAS  PubMed  Google Scholar 

  42. Lee C, Wevrick R, Fisher RB, Ferguson-Smith MA, Lin CC (1997) Human centromeric DNAs.Hum Genet100: 291–304

    Article  CAS  PubMed  Google Scholar 

  43. Kipling D, Warburton PE (1997) Centromeres, CENP-B and Tigger too.Trends Genet13: 141–145

    Article  CAS  PubMed  Google Scholar 

  44. Tyler-Smith C, Corish P, Burns E (1998) Neocentromeres, theY chromosome and centromere evolution.Chromosome Res6: 65–71

    Article  CAS  PubMed  Google Scholar 

  45. Harrington JJ, Van Bokkelen G, Mays RW, Gustashaw K, Willard HF (1997) Formation ofde novacentromeres and construction of first-generation human artificial microchromosomes.Nat Genet15: 345–355

    Article  CAS  PubMed  Google Scholar 

  46. Goldberg IG, Sawhney H, Pluta AF, Warburton PE, Earnshaw WC (1996) Surprising deficiency of CENP-B binding-sites in African-green monkey alpha-satellite DNA — implications for CENP-B function at centromeres.Mol Cell Biol16: 5156–5168

    CAS  PubMed  Google Scholar 

  47. Harrison GE, Heslop-Harrison JS (1995) Centromeric repetitive DNA in the genusBrassica. TheorAppl Genet90: 157–165

    CAS  Google Scholar 

  48. Brandes A, Thompson H, Dean C, Heslop-Harrison JS (1997) Multiple repetitive DNA sequences in the paracentromeric regions ofArabidopsis thalianaL.Chromosome Res5: 238–246

    Article  CAS  PubMed  Google Scholar 

  49. Galasso I, Schmidt T, Pignone D, Heslop-Harrison JS (1995) The molecular cytogenetics ofVigna unguiculata(L.) Walp: the physical organization and characterization of 18S-5.8S–25S rRNA genes, 5S rRNA genes, telomere-like sequences, and a family of centromeric repetitive DNA sequences.Theor Appl Genet91: 928–935

    Article  CAS  Google Scholar 

  50. Leach CR, Donald TM, Franks TK, Spiniello SS, Hanrahan CF, Timmis JN (1995) Organization and origin of a B chromosome centromeric sequence fromBrachycome dichromosomatica. Chromosoma103: 708–714

    Article  CAS  Google Scholar 

  51. Aragon-Alcaide L, Miller T, Schwarzacher T, Reader S, Moore G (1996) A cereal centromeric sequence.Chromosoma105: 261–268

    Article  CAS  PubMed  Google Scholar 

  52. Jiang J, Nasuda S, Dong F, Scherrer CW, Woo S-S, Wing RA, Gill BS, Ward DC (1996) A conserved repetitive DNA element located in the centromeres of cereal chromosomes.Proc Natl Acad Sci USA93: 14210–14213

    Article  CAS  PubMed  Google Scholar 

  53. Nagaki K, Tsujimoto H, Sasakuma T (1998) A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions.Chromosome Res6: 295–302

    Article  CAS  PubMed  Google Scholar 

  54. Maluszynska J, Heslop-Harrison JS (1991) Localization of tandemly repeated DNA sequences inArabidopsis thaliana. Plant J1: 159–166

    Google Scholar 

  55. Murata M, Ogura Y, Motoyoshi F (1994) Centromeric repetitive sequences inArabidopsis thaliana. Jpn J Genet69: 361–370

    CAS  Google Scholar 

  56. Pelissier T, Tutois S, Tourmente S, Deragon JM, Picard G (1996) DNA regions flanking the majorArabidopsis thalianasatellite are principally enriched in Athila retroelement sequences.Genetica97: 141–151

    Article  CAS  PubMed  Google Scholar 

  57. Kamm A, Galasso I, Schmidt T, Heslop-Harrison JS (1995) Analysis of a repetitive DNA family fromArabidopsis arenosaand relationships betweenArabidopsisspecies.Plant Mol Biol27: 853–862

    Article  CAS  PubMed  Google Scholar 

  58. Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A TY3/GYPSY retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes.Plant J16: 721–728

    Article  CAS  PubMed  Google Scholar 

  59. Finch JT, Klug A (1976) Solenoid model for superstructure in chromatinProc Natl Acad Sci USA73: 1897–1901

    Article  CAS  PubMed  Google Scholar 

  60. Vershinin AV, Heslop-Harrison JS (1998) Comparative analysis of the nucleosomal structure of rye, wheat and their relatives.Plant Mol Biol36: 149–161

    Article  CAS  PubMed  Google Scholar 

  61. Meyne J, Ratliff RL, Buckingham JM, Jones MD, Wilson JS, Moyzis RK (1990) The human telomere.Chromosome Today10: 75–80

    Google Scholar 

  62. Biessmann H, Walter MF, Kurenova E, Mason JM (1993) Retrotransposons atDrosophilatelomeres and terminal chromosome deficiencies.Chromosome Today12: 104–121

    Google Scholar 

  63. Richards EJ, Vongs A, Walsh M, Yang J, Chao S (1993) Substructure of telomere repeat arrays. In: JS Heslop-Harrison, RB Flavell (eds):The Chromosome.Bios, Oxford, 103–114

    Google Scholar 

  64. Fuchs J, Brandes A, Schubert I (1995) Telomere sequence localization and karyotype evolution in higher plants.Plant Syst Evol196: 227–241

    Article  CAS  Google Scholar 

  65. Greider CW, Autexier C, Avilion AA, Collins K, Harrington LA, Mantell LL, Prowse KR, Smith SK, Allsopp RC, Counter CM et al (1993) Telomeres and telomerase in mortal and immortal cells. In: JS Heslop-Harrison, RB Flavell (eds):The Chromosome.Bios, Oxford, 115–125

    Google Scholar 

  66. Schmidt T, Heslop-Harrison JS (1996) The physical and genomic organization of microsatellites in sugar beet.Proc Natl Acad Sci USA93: 8761–8765

    Article  CAS  PubMed  Google Scholar 

  67. Cuadrado A, Schwarzacher T (1999) The chromosomal organization of simple sequence repeats in wheat and rye genomes.Chromosoma107: 587–594

    Article  Google Scholar 

  68. Schmidt T, Heslop-Harrison JS (1998) Genomes, genes and junk: the large scale organization of plant chromosomes.Trends Plant Sci3: 195–199

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Cell Biology, John Innes Centre, Norwich, NR4 7UJ, UK

    J. S. Heslop-Harrison

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  1. J. S. Heslop-Harrison
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Editors and Affiliations

  1. Istituto di Biologia e Genetica, Via Brecce Bianche, Ancona, 60131, Italy

    Ettore Olmo

  2. Dipartimento di Biologia animale / Centro di Studio per l’Istochimica — CNR, University of Pavia, Piazza Botta 9, Pavia, 27100, Italy

    Carlo Alberto Redi

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Heslop-Harrison, J.S. (2000). RNA, genes, genomes and chromosomes: repetitive DNA sequences in plants. In: Olmo, E., Redi, C.A. (eds) Chromosomes Today. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8484-6_4

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  • DOI: https://doi.org/10.1007/978-3-0348-8484-6_4

  • Publisher Name: Birkhäuser, Basel

  • Print ISBN: 978-3-0348-9587-3

  • Online ISBN: 978-3-0348-8484-6

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