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Genetics. Feb 2000; 154(2): 869–884.
PMCID: PMC1460944

De novo evolution of satellite DNA on the rye B chromosome.

Abstract

The most distinctive region of the rye B chromosome is a subtelomeric domain that contains an exceptional concentration of B-chromosome-specific sequences. At metaphase this domain appears to be the physical counterpart of the subtelomeric heterochromatic regions present on standard rye chromosomes, but its conformation at interphase is less condensed. In this report we show that the two sequence families that have been previously found to make up the bulk of the domain have been assembled from fragments of a variety of sequence elements, giving rise to their ostensibly foreign origin. A single mechanism, probably based on synthesis-dependent strand annealing (SDSA), is responsible for their assembly. We provide evidence for sequential evolution of one family on the B chromosome itself. The extent of these rearrangements and the complexity of the higher-order organization of the B-chromosome-specific families indicate that instability is a property of the domain itself, rather than of any single sequence. Indirect evidence suggests that particular fragments may have been selected to confer different properties on the domain and that rearrangements are frequently selected for their effect on DNA structure. The current organization appears to represent a transient stage in the evolution of a conventional heterochromatic region from complex sequences.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ananiev EV, Phillips RL, Rines HW. Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin. Genetics. 1998 Aug;149(4):2025–2037. [PMC free article] [PubMed]
  • Ananiev EV, Phillips RL, Rines HW. Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):13073–13078. [PMC free article] [PubMed]
  • Avramova Z, Tikhonov A, Chen M, Bennetzen JL. Matrix attachment regions and structural colinearity in the genomes of two grass species. Nucleic Acids Res. 1998 Feb 1;26(3):761–767. [PMC free article] [PubMed]
  • Bennetzen JL, Kellogg EA. Do Plants Have a One-Way Ticket to Genomic Obesity? Plant Cell. 1997 Sep;9(9):1509–1514. [PMC free article] [PubMed]
  • Bennetzen JL, SanMiguel P, Chen M, Tikhonov A, Francki M, Avramova Z. Grass genomes. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1975–1978. [PMC free article] [PubMed]
  • Lima-De-Faria A. Genetic Interaction in Rye Expressed at the Chromosome Phenotype. Genetics. 1962 Oct;47(10):1455–1462. [PMC free article] [PubMed]
  • Best S, Le Tissier P, Towers G, Stoye JP. Positional cloning of the mouse retrovirus restriction gene Fv1. Nature. 1996 Aug 29;382(6594):826–829. [PubMed]
  • Lowary PT, Widom J. Nucleosome packaging and nucleosome positioning of genomic DNA. Proc Natl Acad Sci U S A. 1997 Feb 18;94(4):1183–1188. [PMC free article] [PubMed]
  • Blunden R, Wilkes TJ, Forster JW, Jimenez MM, Sandery MJ, Karp A, Jones RN. Identification of the E3900 family, a second family of rye B chromosome specific repeated sequences. Genome. 1993 Aug;36(4):706–711. [PubMed]
  • Mollegaard NE, Bailly C, Waring MJ, Nielsen PE. Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3'-A-tract junction. Nucleic Acids Res. 1997 Sep 1;25(17):3497–3502. [PMC free article] [PubMed]
  • Brukner I, Sánchez R, Suck D, Pongor S. Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data. J Biomol Struct Dyn. 1995 Oct;13(2):309–317. [PubMed]
  • Morais-Cecílio L, Delgado M, Jones RN, Viegas W. Interphase arrangement of rye B chromosomes in rye and wheat. Chromosome Res. 1997 May;5(3):177–181. [PubMed]
  • Caizzi R, Caggese C, Pimpinelli S. Bari-1, a new transposon-like family in Drosophila melanogaster with a unique heterochromatic organization. Genetics. 1993 Feb;133(2):335–345. [PMC free article] [PubMed]
  • Craig JM, Boyle S, Perry P, Bickmore WA. Scaffold attachments within the human genome. J Cell Sci. 1997 Nov;110(Pt 21):2673–2682. [PubMed]
  • Müller HP, Varmus HE. DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes. EMBO J. 1994 Oct 3;13(19):4704–4714. [PMC free article] [PubMed]
  • Csink AK, Henikoff S. Something from nothing: the evolution and utility of satellite repeats. Trends Genet. 1998 May;14(5):200–204. [PubMed]
  • Munteanu MG, Vlahovicek K, Parthasarathy S, Simon I, Pongor S. Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena. Trends Biochem Sci. 1998 Sep;23(9):341–347. [PubMed]
  • Dernburg AF, Sedat JW, Hawley RS. Direct evidence of a role for heterochromatin in meiotic chromosome segregation. Cell. 1996 Jul 12;86(1):135–146. [PubMed]
  • Nagaki K, Tsujimoto H, Sasakuma T. Dynamics of tandem repetitive Afa-family sequences in Triticeae, wheat-related species. J Mol Evol. 1998 Aug;47(2):183–189. [PubMed]
  • Nassif N, Penney J, Pal S, Engels WR, Gloor GB. Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair. Mol Cell Biol. 1994 Mar;14(3):1613–1625. [PMC free article] [PubMed]
  • Fitzgerald DJ, Dryden GL, Bronson EC, Williams JS, Anderson JN. Conserved patterns of bending in satellite and nucleosome positioning DNA. J Biol Chem. 1994 Aug 19;269(33):21303–21314. [PubMed]
  • Gabrielian A, Pongor S. Correlation of intrinsic DNA curvature with DNA property periodicity. FEBS Lett. 1996 Sep 9;393(1):65–68. [PubMed]
  • Goodsell DS, Dickerson RE. Bending and curvature calculations in B-DNA. Nucleic Acids Res. 1994 Dec 11;22(24):5497–5503. [PMC free article] [PubMed]
  • Gorbunova V, Levy AA. Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucleic Acids Res. 1997 Nov 15;25(22):4650–4657. [PMC free article] [PubMed]
  • Ostashevsky JY. Centromeric locations in karyotypes: a rule derived from the theory of branched polymers. J Theor Biol. 1996 Aug 7;181(3):293–298. [PubMed]
  • Pan WH, Houben A, Schlegel R. Highly effective cell synchronization in plant roots by hydroxyurea and amiprophos-methyl or colchicine. Genome. 1993 Apr;36(2):387–390. [PubMed]
  • Panstruga R, Büschges R, Piffanelli P, Schulze-Lefert P. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 1998 Feb 15;26(4):1056–1062. [PMC free article] [PubMed]
  • Pasero P, Sjakste N, Blettry C, Got C, Marilley M. Long-range organization and sequence-directed curvature of Xenopus laevis satellite 1 DNA. Nucleic Acids Res. 1993 Oct 11;21(20):4703–4710. [PMC free article] [PubMed]
  • Presting GG, Malysheva L, Fuchs J, Schubert I. A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J. 1998 Dec;16(6):721–728. [PubMed]
  • Houben A, Kynast RG, Heim U, Hermann H, Jones RN, Forster JW. Molecular cytogenetic characterisation of the terminal heterochromatic segment of the B-chromosome of rye (Secale cereale). Chromosoma. 1996 Aug;105(2):97–103. [PubMed]
  • Pruss D, Bushman FD, Wolffe AP. Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):5913–5917. [PMC free article] [PubMed]
  • Kipling D, Warburton PE. Centromeres, CENP-B and Tigger too. Trends Genet. 1997 Apr;13(4):141–145. [PubMed]
  • Vershinin AV, Heslop-Harrison JS. Comparative analysis of the nucleosomal structure of rye, wheat and their relatives. Plant Mol Biol. 1998 Jan;36(1):149–161. [PubMed]
  • Rossi MS, Pesce CG, Reig OA, Kornblihtt AR, Zorzópulos J. Retroviral-like features in the monomer of the major satellite DNA from the South American rodents of the genus Ctenomys. DNA Seq. 1993;3(6):379–381. [PubMed]
  • Vershinin AV, Schwarzacher T, Heslop-Harrison JS. The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes. Plant Cell. 1995 Nov;7(11):1823–1833. [PMC free article] [PubMed]
  • Rubin E, Levy AA. Abortive gap repair: underlying mechanism for Ds element formation. Mol Cell Biol. 1997 Nov;17(11):6294–6302. [PMC free article] [PubMed]
  • Vershinin AV, Alkhimova EG, Heslop-Harrison JS. Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some Triticeae species. Chromosome Res. 1996 Nov;4(7):517–525. [PubMed]
  • Salomon S, Puchta H. Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells. EMBO J. 1998 Oct 15;17(20):6086–6095. [PMC free article] [PubMed]
  • Wallrath LL, Elgin SC. Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev. 1995 May 15;9(10):1263–1277. [PubMed]
  • Salser W, Bowen S, Browne D, el-Adli F, Fedoroff N, Fry K, Heindell H, Paddock G, Poon R, Wallace B, et al. Investigation of the organization of mammalian chromosomes at the DNA sequence level. Fed Proc. 1976 Jan;35(1):23–35. [PubMed]
  • Wessler S, Tarpley A, Purugganan M, Spell M, Okagaki R. Filler DNA is associated with spontaneous deletions in maize. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8731–8735. [PMC free article] [PubMed]
  • Sánchez-Alonso P, Guzmán P. Organization of chromosome ends in Ustilago maydis. RecQ-like helicase motifs at telomeric regions. Genetics. 1998 Mar;148(3):1043–1054. [PMC free article] [PubMed]
  • Wilkes TM, Francki MG, Langridge P, Karp A, Jones RN, Forster JW. Analysis of rye B-chromosome structure using fluorescence in situ hybridization (FISH). Chromosome Res. 1995 Dec;3(8):466–472. [PubMed]
  • Yamada M, Hayatsu N, Matsuura A, Ishikawa F. Y'-Help1, a DNA helicase encoded by the yeast subtelomeric Y' element, is induced in survivors defective for telomerase. J Biol Chem. 1998 Dec 11;273(50):33360–33366. [PubMed]
  • Smith GP. Evolution of repeated DNA sequences by unequal crossover. Science. 1976 Feb 13;191(4227):528–535. [PubMed]
  • Young MA, Srinivasan J, Goljer I, Kumar S, Beveridge DL, Bolton PH. Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG). Methods Enzymol. 1995;261:121–144. [PubMed]
  • Taniguchi M, Sugiyama T. Isolation, characterization and expression of cDNA clones encoding a mitochondrial malate translocator from Panicum miliaceum L. Plant Mol Biol. 1996 Jan;30(1):51–64. [PubMed]
  • Yu HG, Hiatt EN, Chan A, Sweeney M, Dawe RK. Neocentromere-mediated chromosome movement in maize. J Cell Biol. 1997 Nov 17;139(4):831–840. [PMC free article] [PubMed]
  • Tatout C, Lavie L, Deragon JM. Similar target site selection occurs in integration of plant and mammalian retroposons. J Mol Evol. 1998 Oct;47(4):463–470. [PubMed]
  • Tenzen T, Matsuda Y, Ohtsubo H, Ohtsubo E. Transposition of Tnr1 in rice genomes to 5'-PuTAPy-3' sites, duplicating the TA sequence. Mol Gen Genet. 1994 Nov 15;245(4):441–448. [PubMed]

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