Coexistence of NtCENH3 and two retrotransposons in tobacco centromeres

Chromosome Research

Volumn 19, Issue 5, 2011, Pages 591-605

  Nagaki, Kiyotaka ^a   Shibata, Fukashi ^a   Suzuki, Go ^b   Kanatani, Asaka ^a   Ozaki, Souichi ^a   Hironaka, Akiko ^a   Kashihara, Kazunari ^a   Murata, Minoru ^a  

^a OKAYAMA UNIVERSITY   (Japan)

^b OSAKA KYOIKU UNIVERSITY   (Japan)

Author keywords

BAC; centromere; chromatin immunoprecipitation; Nicotiana; retrotransposon; tobacco

Indexed keywords

ANTIBODY; CENTROMERE SPECIFIC HISTONE H3; DNA FRAGMENT; HISTONE H3; UNCLASSIFIED DRUG;

ARTICLE; CENTROMERE; DIPLOIDY; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; MOLECULAR CLONING; NICOTIANA SYLVESTRIS; NICOTIANA TOMENTOSIFORMIS; NONHUMAN; PLANT CELL; PLANT CHROMOSOME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; RETROPOSON; TOBACCO;

BLOTTING, SOUTHERN; CELL LINE; CENTROMERE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; DNA, PLANT; HISTONES; IMMUNOPRECIPITATION; IN SITU HYBRIDIZATION, FLUORESCENCE; POLYMERASE CHAIN REACTION; PROTEIN BINDING; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; TOBACCO;

BACTERIA (MICROORGANISMS); LYCOPERSICON ESCULENTUM; NICOTIANA; NICOTIANA SYLVESTRIS; NICOTIANA TABACUM; NICOTIANA TOMENTOSIFORMIS;

EID: 80052435478     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-011-9219-2     Document Type: Article

References (42)

1. L Aragon-Alcaide T Miller T Schwarzacher S Reader G Moore 1996 A cereal centromeric sequence Chromosoma 105 261 268 8939818 10.1007/BF02524643 1:CAS:528:DyaK2sXhsVeqtLs%3D (Pubitemid 27029691)
2. SB Chang TJ Yang E Datema J van Vugt B Vosman A Kuipers M Meznikova D Szinay RK Lankhorst E Jacobsen H de Jong 2008 FISH mapping and molecular organization of the major repetitive sequences of tomato Chromosome Res 16 919 933 18688733 10.1007/s10577-008-1249-z 1:CAS:528:DC%2BD1cXht12lsLfJ
3. Z Cheng F Dong T Langdon S Ouyang CR Buell M Gu FR Blattner J Jiang 2002 Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon Plant Cell 14 1691 1704 12172016 10.1105/tpc.003079 1:CAS:528:DC%2BD38XmslChurY%3D (Pubitemid 35002929)
4. Choo KHA (1997) The centromere. Oxford University Press, Oxford
5. L Clarke J Carbon 1983 Genomic substitutions of centromeres in Saccharomyces cerevisiae Nature 305 23 28 6350891 10.1038/305023a0 1:CAS:528:DyaL3sXlsFeitr8%3D (Pubitemid 13041970)
6. JJ Clarkson KY Lim A Kovarik MW Chase S Knapp AR Leitch 2005 Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae) New Phytol 168 241 252 16159337 10.1111/j.1469-8137.2005.01480.x 1:CAS:528:DC%2BD2MXhtFeksLfE
7. KM Devos JK Brown JL Bennetzen 2002 Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis Genome Res 12 1075 1079 12097344 10.1101/gr.132102 1:CAS:528:DC%2BD38XlsVWgsr0%3D (Pubitemid 34785200)
8. H Hirochika H Otsuki M Yoshikawa Y Otsuki K Sugimoto S Takeda 1996 Autonomous transposition of the tobacco retrotransposon Tto1 in rice Plant Cell 8 725 734 8624443 10.1105/tpc.8.4.725 1:CAS:528:DyaK28Xis1Grt78%3D (Pubitemid 126632553)
9. T Hosouchi N Kumekawa H Tsuruoka H Kotani 2002 Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3 DNA Res 9 117 121 12240833 10.1093/dnares/9.4.117 1:CAS:528:DC%2BD38XntVSisLg%3D (Pubitemid 36307034)
10. A Houben E Schroeder-Reiter K Nagaki S Nasuda G Wanner M Murata TR Endo 2007 CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley Chromosoma 116 275 283 17483978 10.1007/s00412-007-0102-z 1:CAS:528:DC%2BD2sXntl2mu7s%3D (Pubitemid 46712016)
11. S Hudakova W Michalek GG Presting R ten Hoopen K dos Santos Z Jasencakova I Schubert 2001 Sequence organization of barley centromeres Nucleic Acids Res 29 5029 5035 11812833 10.1093/nar/29.24.5029 1:CAS:528:DC%2BD38XmslWgtA%3D%3D (Pubitemid 34065418)
12. International Human Genome Sequencing Consortium 2001 Initial sequencing and analysis of the human genome Nature 409 860 921 10.1038/35057062 (Pubitemid 32165345)
13. International Rice Genome Sequencing Project 2005 The map-based sequence of the rice genome Nature 436 793 800 10.1038/nature03895 (Pubitemid 41160631)
14. J Jiang S Nasuda F Dong CW Scherrer S Woo RA Wing BS Gill DC Ward 1996 A conserved repetitive DNA element located in the centromeres of cereal chromosomes Proc Natl Acad Sci USA 93 14210 14213 8943086 10.1073/pnas.93.24. 14210 1:CAS:528:DyaK28Xnt1Grsbw%3D (Pubitemid 26424271)
15. J Jiang JA Birchler WA Parrott RK Dawe 2003 A molecular view of plant centromeres Trends Plant Sci 8 570 575 14659705 10.1016/j.tplants.2003.10.011 1:CAS:528:DC%2BD3sXpsVSltbg%3D (Pubitemid 38038930)
16. W Jin JR Melo K Nagaki PB Talbert S Henikoff RK Dawe J Jiang 2004 Maize centromeres: organization and functional adaptation in the genetic background of oat Plant Cell 16 571 581 14973167 10.1105/tpc.018937 1:CAS:528: DC%2BD2cXisFGkt78%3D (Pubitemid 38335271)
17. Kato K, Matsumoto T, Koiwai A, Mizusaki S, Nishida K, Noguchi M, Tamaki E (1972) Liquid suspension culture of tobacco cells. In: Terui G (ed) Fermentation technology today. Osaka, Society of Fermentation Technology of Japan, pp 689-695
18. U-J Kim BW Birren T Slepak V Mancino C Boysen H-L Kang MI Simon H Shizuya 1996 Construction and characterization of a human bacterial artificial chromosome library Genomics 34 213 218 8661051 10.1006/geno.1996.0268 1:CAS:528:DyaK28XjsFOru78%3D (Pubitemid 26172844)
19. N Kumekawa T Hosouchi H Tsuruoka H Kotani 2000 The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 5 DNA Res 7 315 321 11214966 10.1093/dnares/7.6.315 1:CAS:528:DC%2BD3MXpsVOntw%3D%3D
20. N Kumekawa T Hosouchi H Tsuruoka H Kotani 2001 The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4 DNA Res 8 285 290 11853315 10.1093/dnares/8.6.285 1:CAS:528:DC%2BD38XhtFGhsLo%3D (Pubitemid 33617881)
21. H Lee W Zhang T Langdon W Jin H Yan Z Cheng J Jiang 2005 Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species Proc Natl Acad Sci USA 102 11793 11798 16040802 10.1073/pnas.0503863102 1:CAS:528:DC%2BD2MXpsFGgtLY%3D (Pubitemid 41170804)
22. KY Lim K Skalicka B Koukalova RA Volkov R Matyasek V Hemleben AR Leitch A Kovarik 2004 Dynamic changes in the distribution of a satellite homologous to intergenic 26-18S rDNA spacer in the evolution of Nicotiana Genetics 166 1935 1946 15126410 10.1534/genetics.166.4.1935 1:CAS:528:DC%2BD2cXkvF2gs7c%3D (Pubitemid 38621072)
23. Z Liu W Yue D Li RR Wang X Kong K Lu G Wang Y Dong W Jin X Zhang 2008 Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres Chromosoma 117 445 456 18496705 10.1007/s00412-008-0161-9 1:CAS:528:DC%2BD1cXhtV2jsbrL
24. HS Malik S Henikoff 2002 Conflict begets complexity: the evolution of centromeres Curr Opin Genet Dev 12 711 718 12433586 10.1016/S0959-437X(02)00351- 9 1:CAS:528:DC%2BD38XosFOhs7s%3D (Pubitemid 35335991)
25. EA Moscone MA Matzke AJ Matzke 1996 The use of combined FISH/GISH in conjunction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco Chromosoma 105 231 236 10.1007/BF02528771 1:CAS:528:DyaK28XnsFynt7o%3D
26. M Murata 2002 Telomeres and centromeres in plants Curr Genet 3 527 538 1:CAS:528:DC%2BD38Xos1Gjsrs%3D (Pubitemid 35331907)
27. K Nagaki M Murata 2005 Characterization of CENH3 and centromere- associated DNA sequences in sugarcane Chromosome Res 13 195 203 15861308 10.1007/s10577-005-0847-2 1:CAS:528:DC%2BD2MXjslOls7g%3D (Pubitemid 40645904)
28. K Nagaki PB Talbert CX Zhong RK Dawe S Henikoff J Jiang 2003 Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres Genetics 163 1221 1225 12663558 1:CAS:528:DC%2BD3sXjtlOgsLs%3D (Pubitemid 36417961)
29. K Nagaki J Song RM Stuper AS Parokonny Q Yuan S Ouyang J Liu J Hsiao KM Jones RK Dawe CR Buell J Jiang 2003 Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres Genetics 163 759 770 12618412 1:CAS:528:DC%2BD3sXislWjurg%3D (Pubitemid 36314556)
30. K Nagaki Z Cheng S Ouyang PB Talbert M Kim KM Jones S Henikoff CR Buell J Jiang 2004 Sequencing of a rice centromere uncovers active genes Nat Genet 36 138 145 14716315 10.1038/ng1289 1:CAS:528:DC%2BD2cXntlCgsA%3D%3D (Pubitemid 38174371)
31. K Nagaki P Neumann D Zhang S Ouyang CR Buell Z Cheng J Jiang 2005 Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice Mol Biol Evol 22 845 855 15616142 10.1093/molbev/msi069 1:CAS:528:DC%2BD2MXjtFais7o%3D (Pubitemid 40471399)
32. K Nagaki K Kashihara M Murata 2009 A centromeric DNA sequence colocalized with a centromere-specific histone H3 in tobacco Chromosoma 118 249 257 19048266 10.1007/s00412-008-0193-1 1:CAS:528:DC%2BD1MXivVGjs78%3D
33. Nagaki K, Walling J, Hirsch C, Jiang J, Murata M (2009b) Structure and evolution of plant centromeres. In: Ugarkovic D (ed) Centromere, progress in molecular and subcellular biology. Springer, Berlin, pp 153-179
34. T Pelissier S Tutois JM Deragon S Tourmente S Genestier G Picard 1995 Athila, a new retroelement from Arabidopsis thaliana Plant Mol Biol 29 441 452 8534844 10.1007/BF00020976 1:CAS:528:DyaK28Xit1aqsQ%3D%3D (Pubitemid 3012221)
35. M Petit KY Lim E Julio C Poncet FDD Borne A Kovarik AR Leitch M-A Grandbastien C Mhiri 2007 Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum) Mol Genet Genomics 278 1 15 17375323 10.1007/s00438-007-0226-0 1:CAS:528:DC%2BD2sXmtlGktLs%3D (Pubitemid 46911427)
36. G Suzuki M Watanabe K Toriyama A Isogai K Hinata 1997 Direct cloning of the Brassica S locus by using a P1-derived artificial chromosome (PAC) vector Gene 199 133 137 9358048 10.1016/S0378-1119(97)00358-2 1:CAS:528: DyaK2sXmvFWjur0%3D (Pubitemid 27448210)
37. AL Tek K Kashihara M Murata K Nagaki 2010 Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon Chromosome Res 18 337 347 20204495 10.1007/s10577-010-9119-x 1:CAS:528:DC%2BC3cXkslSgt70%3D
38. The Arabidopsis Genome Initiative 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 796 815 10.1038/35048692 (Pubitemid 32016083)
39. TK Wolfgruber A Sharma KL Schneider PS Albert D-H Koo J Shi Z Gao F Han H Lee R Xu J Allison JA Birchler J Jiang RK Dawe GG Presting 2009 Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic loci shaped primarily by retrotransposons PLoS Genet 5 e1000743 19956743 10.1371/journal.pgen.1000743
40. F Wu SD Tanksley 2010 Chromosomal evolution in the plant family Solanaceae BMC Genomics 11 182 20236516 10.1186/1471-2164-11-182
41. H Yan H Ito K Nobuta S Ouyang W Jin S Tian C Lu RC Venu GL Wang PJ Green RA Wing CR Buell BC Meyers J Jiang 2006 Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere Plant Cell 18 2123 2133 16877494 10.1105/tpc.106.043794 1:CAS:528:DC%2BD28XhtVKgurjL (Pubitemid 44484714)
42. CX Zhong JB Marshall C Topp R Mroczek A Kato K Nagaki JA Birchler J Jiang RK Dawe 2002 Centromeric retroelements and satellites interact with maize kinetochore protein CENH3 Plant Cell 14 2825 2836 12417704 10.1105/tpc.006106 1:CAS:528:DC%2BD38XovF2qurg%3D (Pubitemid 35326307)