Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice

Molecular Biology and Evolution

Volumn 23, Issue 12, 2006, Pages 2505-2520

  Lee, Hye Ran ^a   Neumann, Pavel ^a   Macas, Jiri ^b   Jiang, Jiming ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b INSTITUTE OF PLANT MOLECULAR BIOLOGY   (Czech Republic)

Author keywords

Centromere; Satellite repeat; siRNA; Transcription

Indexed keywords

SATELLITE DNA; SMALL INTERFERING RNA;

ARTICLE; CENTROMERE; CHROMATIN; CONTROLLED STUDY; EPIGENETICS; EUKARYOTE; HETEROCHROMATIN; IMMUNOPRECIPITATION; MOLECULAR CLONING; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; RICE;

BASE SEQUENCE; BINDING SITES; CENTROMERE; CHROMOSOMES, PLANT; CLONING, MOLECULAR; DNA, PLANT; DNA, SATELLITE; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

EUKARYOTA;

EID: 33750932803     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl127     Document Type: Article

References (65)

1. Ananiev EV, Phillips RL, Rines HW. 1998. Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA. 95:13073-13078.
2. Ando S, Yang H, Nozaki N, Okazaki T, Yoda K. 2002. CENP-A, -B, and -C chromatin complex that contains the I-type alpha-satellite array constitutes the prekinetochore in HeLa cells. Mol Cell Biol. 22:2229-2241.
3. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T. 2003. The small RNA profile during Drosophila melanogaster development. Dev Cell. 5:337-350.
4. Baldwin L, Macgregor HC. 1985. Centromeric satellite DNA in the newt Triturus cristatus karelinii and related species: its distribution and transcription on lampbrush chromosomes. Chromosoma. 92:100-107.
5. Bernstein E, Allis CD. 2005. RNA meets chromatin. Genes Dev. 19:1635-1655.
6. Charlesworth B, Sniegowski P, Stephan W. 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature. 371:215-220.
7. Cheng ZK, Dong F, Langdon T, Ouyang S, Buell CB, Gu MH, Blattner FR, Jiang J. 2002. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retro-transposon. Plant Cell. 14:1691-1704.
8. Choo KHA. 2000. Centromerization. Trends Cell Biol. 10: 182-188.
9. Cooper JL, Henikoff S. 2004. Adaptive evolution of the histone fold domain in centromeric histones. Mol Biol Evol. 21:1712-1718.
10. de la Herran R, Fontana F, Lanfredi M, Congiu L, Leis M, Rossi R, Rejon CR, Rejon MR, Garrido-Ramos MA. 2001. Slow rates of evolution and sequence homogenization in an ancient satellite DNA family of sturgeons. Mol Biol Evol. 18:432-436.
11. Dong F, Miller JT, Jackson SA, Wang GL, Ronald PC, Jiang J. 1998. Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc Natl Acad Sci USA. 95:8135-8140.
12. Dover G. 1982. Molecular drive: a cohesive mode of species evolution. Nature. 299:111-117.
13. Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, Nakayama T, Oshimura M. 2004. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol. 6:784-791.
14. Gendrel AV, Colot V. 2005. Arabidopsis epigenetics: when RNA meets chromatin. Curr Opin Plant Biol. 8:142-147.
15. Hall IM, Shankaranarayana GD, Noma KI, Ayoub N, Cohen A, Grewal SIS. 2002. Establishment and maintenance of a heterochromatin domain. Science. 297:2232-2237.
16. Hall SE, Kettler G, Preuss D. 2003. Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains. Genome Res. 13:195-205.
17. Hall SE, Luo S, Hall AE, Preuss D. 2005. Differential rates of local and global homogenization in centromere satellites from Arabidopsis relatives. Genetics. 170:1913-1927.
18. Henikoff S, Ahmad K, Malik HS. 2001. The centromere paradox: stable inheritance with rapidly evolving DNA. Science. 293:1098-1102.
19. Herzel H, Weiss O, Trifonov EN. 1999. 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics. 15:187-193.
20. Heslop-Harrison JS, Murata M, Ogura Y, Schwarzacher T, Motoyoshi F. 1999. Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes. Plant Cell. 11:31-42.
21. Jiang J, Birchler JB, Parrott WA, Dawe RK. 2003. A molecular view of plant centromeres. Trends Plant Sci. 8:570-575.
22. Jin WW, Lamb JC, Vega JM, Dawe RK, Birchler JA, Jiang J. 2005. Molecular and functional dissection of the maize B centromere. Plant Cell. 17:1412-1423.
23. Jin WW, Melo JR, Nagaki K, Talbert PB, Henikoff S, Dawe RK, Jiang J. 2004. Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell. 16:571-581.
24. Kanellopoulou C, Muljo SA, Kung AL, Ganesan S, Drapkin R, Jenuwein T, Livingston DM, Rajewsky K. 2005. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 19:489-501.
25. Kumekawa N, Hosouchi T, Tsuruoka H, Kotani H. 2000. The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 5. DNA Res. 7:315-321.
26. Kumekawa N, Hosouchi T, Tsuruoka H, Kotani H. 2001. The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4. DNA Res. 8:285-290.
27. Lamb JC, Kato A, Birchler JA. 2005. Sequences associated with A chromosome centromeres are present throughout the maize B chromosome. Chromosoma. 113:337-349.
28. Lee HR, Zhang WL, Langdon T, Jin WW, Yan HH, Cheng ZK, Jiang J. 2005. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci USA. 102:11793-11798.
29. Lu C, Tej SS, Luo SJ, Haudenschild CD, Meyers BC, Green PJ. 2005. Elucidation of the small RNA component of the transcriptome. Science. 309:1567-1569.
30. Ma J, Jackson SA. 2006. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res. 16: 251-259.
31. Macas J, Navratilova A, Koblizkova A. 2006. Sequence homogenization and chromosomal localization of VicTR-B satellites differ between closely related Vicia species. Chromosoma 10.1007/s00412-006-0070-8.
32. Malik HS, Henikoff S. 2001. Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics. 157:1293-1298.
33. Malik HS, Henikoff S. 2002. Conflict begets complexity: the evolution of centromeres. Curr Opin Genet Dev. 12:711-718.
34. Martens JHA, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, Steinlein P, Jenuwein T. 2005. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 24:800-812.
35. Masumoto H, Masukata H, Muro Y, Nozaki N, Okazaki T. 1989. A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. J Cell Biol. 109:1963-1973.
36. Matsumoto T, Wu JZ, Kanamori H, et al. (260 co-authors). 2005. The map-based sequence of the rice genome. Nature. 436: 793-800.
37. May BP, Lippman ZB, Fang YD, Spector DL, Martienssen RA. 2005. Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet. 1: 705-714.
38. Mravinac B, Plohl M, Ugarkovic D. 2005. Preservation and high sequence conservation of satellite DNAs suggest functional constraints. J Mol Evol. 61:542-550.
39. Nagaki K, Cheng ZK, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J. 2004. Sequencing of a rice centromere uncovers active genes. Nat Genet. 36:138-145.
40. Oakey R, Tyler-Smith C. 1990. Y chromosome DNA haplotyping suggests that most European and Asian men are descended from one of two males. Genomics. 7:325-330.
41. Ohzeki J, Nakano M, Okada T, Masumoto H. 2002. CENP-B box is required for de novo centromere chromatin assembly on human alphoid DNA. J Cell Biol. 159:765-775.
42. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16: 276-277.
43. Rudd MK, Willard HF. 2004. Analysis of the centromeric regions of the human genome assembly. Trends Genet. 20: 529-533.
44. Rudd MK, Wray GA, Willard HF. 2006. The evolutionary dynamics of α-satellite. Genome Res. 16:88-96.
45. Schueler MG, Dunn JM, Bird CP, Ross MT, Viggiano L, Rocchi M, Willard HF, Green ED. 2005. Progressive proximal expansion of the primate X chromosome centromere. Proc Natl Acad Sci USA. 102:10563-10568.
46. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF. 2001. Genomic and genetic definition of a functional human centromere. Science. 294:109-115.
47. Shibata F, Murata M. 2004. Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana. J Cell Sci. 117:2963-2970.
48. Smith GP. 1976. Evolution of repeated DNA sequences by unequal crossover. Science. 191:528-535.
49. Song JQ, Dong FG, Lilly JW, Stupar RM, Jiang JM. 2001. Instability of bacterial artificial chromosome (BAC) clones containing tandemly repeated DNA sequences. Genome. 44: 463-469.
50. Sonnhammer ELL, Durbin R. 1995. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene. 167:GC1-GC10.
51. Spence JM, Critcher R, Ebersole TA, Valdivia MM, Earnshaw WC, Fukagawa T, Farr CJ. 2002. Co-localization of centromere activity, proteins and topoisomerase II within a subdomain of the major human X alpha satellite array. EMBO J. 21:5269-5280.
52. Sunkar R, Girke T, Jain PK, Zhu JK. 2005. Cloning and characterization of microRNAs from rice. Plant Cell. 17:1397-1411.
53. Sunkar R, Girke T, Zhu JK. 2005. Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res. 33:4443-4454.
54. Sutton GG, White O, Adams MD, Kerlavage AR. 1995. TIGR Assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci Technol. 1:9-19.
55. Talbert PB, Bryson TD, Henikoff S. 2004. Adaptive evolution of centromeric proteins in plants and animals. J Biol. 3:18.
56. Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S. 2002. Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell. 14:1053-1066.
57. Terranova R, Sauer S, Merkenschlager M, Fisher AG. 2005. The reorganisation of constitutive heterochromatin in differentiating muscle requires HDAC activity. Exp Cell Res. 310: 344-356.
58. Topp CN, Zhong CX, Dawe RK. 2004. Centromere-encoded RNAs are integral components of the maize kinetochore. Proc Natl Acad Sci USA. 101:15986-15991.
59. Verdel A, Jia ST, Gerber S, Sugiyama T, Gygi S, Grewal SIS, Moazed D. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science. 303:672-676.
60. Volpe T, Schramke V, Hamilton GL, White SA, Teng G, Martienssen RA, Allshire RC. 2003. RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11:137-146.
61. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS, Martienssen RA. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science. 297:1833-1837.
62. Wevrick R, Willard HF. 1989. Long-range organization of tandem arrays of a satellite DNA at the centromeres of human chromosomes: high frequency array-length polymorphism and meiotic stability. Proc Natl Acad Sci USA. 86:9394-9398.
63. Willard HF, Waye JS. 1987. Chromosome-specific subsets of human {alpha} satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat. J Mol Evol. 25:207-214.
64. Wu JZ, Yamagata H, Hayashi-Tsugane M, et al. (21 co-authors). 2004. Composition and structure of the centromeric region of rice chromosome 8. Plant Cell. 16:967-976.
65. Zhang W, Yi C, Bao W, Liu B, Cui J, Yu H, Cao X, Gu M, Liu M, Cheng Z. 2005. The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol. 138:1205-1215.