Distribution of short interstitial telomere motifs in two plant genomes: Putative origin and function

BMC Plant Biology

Volumn 10, Issue , 2010, Pages

  Gaspin, Christine ^a   Rami, Jean François ^b   Lescure, Bernard ^c  

^a CEMAGREF   (France)

^b CIRAD   (France)

^c LABORATOIRE DES INTERACTIONS PLANTES MICROORGANISMES LIPM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; ORYZA SATIVA;

RIBOSOME PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; DNA FLANKING REGION; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GENOME; PROMOTER REGION; REGULATORY SEQUENCE; RICE; TELOMERE;

3' UNTRANSLATED REGIONS; 5' FLANKING REGION; 5' UNTRANSLATED REGIONS; ARABIDOPSIS; BASE SEQUENCE; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PROMOTER REGIONS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; RIBOSOMAL PROTEINS; TELOMERE;

EID: 78651491151     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-10-283     Document Type: Article

References (51)

1. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 2008, (36 Database):D1009-D1014. 2238962, 17986450.
2. Bülow L, Engelmann S, Schindler M, Hehl R. AthaMap, integrating transcriptional and post-transcriptional data. Nucleic Acids Res 2009, (37 Database):D983-D986. 2686474, 18842622.
3. Axelos M, Bardet C, Liboz T, Le Van Thai A, Curie C, Lescure B. The gene family encoding the translation elongation factor eEF1A: molecular cloning, characterization and expression. Mol Gen Genet 1989, 219:106-112. 10.1007/BF00261164, 2615757.
4. Liboz T, Bardet C, Le Van Thai A, Axelos M, Lescure B. The four members of the gene family encoding the translation elongation factor eEF1a are actively transcribed. Plant Mol Biol 1990, 14:107-110. 10.1007/BF00015660, 2101309.
5. Regad F, Hervé C, Marinx O, Bergounioux C, Tremousaygue D, Lescure B. The Tef1 box, an ubiquitous cis-acting element involved in the activation of plant genes that are highly expressed in cycling cells. Mol Gen Genet 1995, 248:703-711. 10.1007/BF02191710, 7476873.
6. Richards E, Ausubel F. Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell 1988, 53:127-136. 10.1016/0092-8674(88)90494-1, 3349525.
7. Hastie ND, Allshire RC. Human telomeres: fusion and interstitial sites. Trends Genet 1989, 5:326-331. 10.1016/0168-9525(89)90137-6, 2692239.
8. Uchida W, Matsunaga S, Sugiyama R, Kawano S. Interstitial telomere-like repeats in the Arabidopsis thaliana genome. Genes Genet Syst 2002, 77:63-67. 10.1266/ggs.77.63, 12036106.
9. Regad F, Lebas M, Lescure B. Interstitial telomere repeats within the Arabidopsis thaliana genome. J Mol Biol 1994, 239:163-169. 10.1006/jmbi.1994.1360, 8196051.
10. Vandepoele K, Casneuf T, Van de Peer Y. Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol 2006, 7:R103. 10.1186/gb-2006-7-11-r103, 1794593, 17090307.
11. Tremousaygue D, Garnier L, Bardet C, Dabos P, Hervé C, Lescure B. Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J 2003, 33:957-966. 10.1046/j.1365-313X.2003.01682.x, 12631321.
12. Manevski A, Bardet C, Tremousaygue D, Lescure B. In synergy with various cis-acting elements, plant interstitial telomere motifs regulate gene expression in Arabidopsis root meristems. FEBS Lett 2000, 483:43-46. 10.1016/S0014-5793(00)02056-1, 11033353.
13. Tremousaygue D, Manevski A, Bardet C, Lescure N, Lescure B. Plant interstitial motifs participate in the control of gene expression in root meristems. Plant J 1999, 20:553-561. 10.1046/j.1365-313X.1999.00627.x, 10652127.
14. Curie C, Liboz T, Bardet C, Gander E, Médale C, Axelos M, Lescure B. Cis- and trans-acting elements involved in the activation of Arabidopsis thaliana A1 gene encoding the translation elongation factor eEF1a. Nucleic Acids Res 1991, 19:1305-1310. 10.1093/nar/19.6.1305, 333858, 1840652.
15. Scheer I, Ludevid M, Regad F, Lescure B, Pont-Lezica R. Expression of a gene encoding a ribosomal p40 protein and identification of an active promoter site. Plant Mol Biol 1997, 35:905-913. 10.1023/A:1005956601270, 9426609.
16. Kosugi S, Ohashi Y. PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. Plant Cell 1997, 9:1607-1619. 10.1105/tpc.9.9.1607, 157037, 9338963.
17. Höfte H, Desprez T, Amselem J, Chiapello H, Caboche M, Moisan A, Jourjon MF, Charpenteau JL, Berthomieu P, Guerrier D, Giraudat J, Quigley F, Thomas F, Yu DY, Mache R, Raynal M, Cooke R, Grellet F, Delseny M, Parmentier Y, Marcillac G, Gigot C, Fleck J, Philipps G, Axelos M, Bardet B, Tremousaygue D, Lescure B. An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J 1993, 4:1041-1061.
18. Cooke R, Raynal M, Laudié M, Grellet F, Delseny M, Morris PC, Guerrier D, Giraudat J, Quigley F, Clabault G, Li YF, Mache R, Krivitzky M, Gy IJJ, Kreis M, Lecharny A, Parmentier Y, Marbach J, Fleck J, Clément B, Philipps G, Hervé C, Bardet C, Tremousaygue D, Lescure B, Lacomme C, Roby D, Jourjon MF, Chabrier P, Charpenteau JL, Desprez T, Amselem J, Chiapello H, Höfte H. Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J 1996, 9:101-124. 10.1046/j.1365-313X.1996.09010101.x, 8580968.
19. Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M. A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 2003, 554:17-22. 10.1016/S0014-5793(03)01041-X, 14596907.
20. Zhang L, Yuan D, Yu S, Li Z, Cao Y, Miao Z, Quian H, Tag K. Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 2004, 20:1081-1086. 10.1093/bioinformatics/bth043, 14764542.
21. Zhang Z, Xue Q. Tri-nucleotide repeats and their association with genes in rice genome. Biosystems 2005, 82:248-256. 10.1016/j.biosystems.2005.08.002, 16226835.
22. Molina C, Grotewold E. Genome wide analysis of Arabidopsis core promoters. BMC Genomics 2005, 6:25. 10.1186/1471-2164-6-25, 554773, 15733318.
23. Yamamoto Y, Ichida H, Abe T, Suzuki Y, Sugano S, Obokata J. Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucleic Acids Res 2007, 35:6219-6226. 10.1093/nar/gkm685, 2094075, 17855401.
24. Grover H, Aishwarya V, Sharma PC. Biased distribution of microsatellite motifs in the rice genome. Mol Genet Genomics 2007, 277:469-480. 10.1007/s00438-006-0204-y, 17237941.
25. Conte MG, Gaillard S, Lanau N, Rouard M, Périn C. GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res 2008, (36 Database):D991-D998. 2238940, 17986457.
26. Liang D, Zhou H, Zhang P, Chen YQ, Chen X, Chen CL, Qu LH. A novel gene organization: intronic snoRNA gene clusters from Oryza sativa. Nucleic Acids Res 2002, 30:3262-3272. 10.1093/nar/gkf426, 135747, 12136108.
27. Chen CL, Liang D, Zhou H, Zhou M, Chen YQ, Qu LH. The high diversity of snoRNAs in plants: Identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Res 2003, 31:2601-2613. 10.1093/nar/gkg373, 156054, 12736310.
28. Santi L, Wang Y, Stile MR, Berendzen K, Wanke D, Roig C, Pozzi C, Muller K, Muller J, Rohde W, Salamini F. The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant J 2003, 34:813-826. 10.1046/j.1365-313X.2003.01767.x, 12795701.
29. Kooiker M, Airoldi CA, Losa A, Manzotti PS, Finzi L, Kater MM, Colombo L. BASIC PENTACYSTEINE1, a GA binding protein that induces conformational changes in the regulatory region of the homeotic Arabidopsis gene SEEDSTICK. Plant Cell 2005, 17:722-729. 10.1105/tpc.104.030130, 1069694, 15722463.
30. Nicolas A. Relationship between transcription and initiation of meiotic recombination: Toward chromatin accessibility. Proc Natl Acad Sci USA 1998, 95:87-89. 10.1073/pnas.95.1.87, 34197, 9419331.
31. Aguilera A. The connection between transcription and genomic instability. EMBO J 2002, 21:195-201. 10.1093/emboj/21.3.195, 125829, 11823412.
32. Drolet M. Growth inhibition mediated by negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology. Mol Microbiol 2006, 59:723-730. 10.1111/j.1365-2958.2005.05006.x, 16420346.
33. Lee M, Blackburn EH. Sequence-specific DNA primer effects on telomerase polymerization activity. Mol Cell Biol 1993, 13:6586-6599. 364717, 8413255.
34. Ren S, Johnston JS, Shippen DE, McKnight TD. Telomerase Activator1 induces telomerase activity and potentiates responses to auxin in Arabidopsis. Plant Cell 2004, 16:2910-2922. 10.1105/tpc.104.025072, 527188, 15486103.
35. Nadir E, Margalit H, Gallily T, Ben-Sasson SA. Microsatellite spreading in the human genome: Evolutionary mechanisms and structural implications. Proc Natl Acad Sci USA 1996, 93:6470-6475. 10.1073/pnas.93.13.6470, 39047, 8692839.
36. Brodniewicz-Proba T, Buchowicz J. Properties of a deoxyribonucleotidyltransferase isolated from wheat germ. Biochem J 1980, 191:139-145. 1162191, 7470090.
37. Gauss GH, Lieber MR. Mechanistic constraints on diversity in human V(D)J recombination. Mol Cell Biol 1996, 16:258-269. 230999, 8524303.
38. Planta RJ, Gonçalves PM, Mager WH. Global regulators of ribosome biosynthesis in yeast. Biochem Cell Biol 1995, 73:825-834. 10.1139/o95-090, 8721998.
39. Hogues H, Lavoie H, Sellam A, Mangos M, Roemer T, Purisima E, Nantel A, Whiteway M. Transcription factor substitution during the evolution of fungal ribosome regulation. Mol Cell 2008, 29:552-562. 10.1016/j.molcel.2008.02.006, 18342603.
40. Hu H, Li X. Transcriptional regulation in eukaryotic ribosomal protein genes. Genomics 2007, 90:421-423. 10.1016/j.ygeno.2007.07.003, 17707610.
41. Curie C, Axelos M, Bardet C, Atanassova R, Chaubet N, Lescure B. Modular organization and developmental activity of an Arabidopsis thaliana eEF1a gene promoter. Mol Gen Genet 1993, 238:428-436. 10.1007/BF00292002, 8492811.
42. Shore D. Telomerase and telomere binding proteins: controlling the endgame. Trends Biochem Sci 1997, 22:233-235. 10.1016/S0968-0004(97)01082-7, 9255061.
43. Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 1999, 24:437-440. 10.1016/S0968-0004(99)01460-7, 10542411.
44. Lieb JD, Liu X, Botstein D, Brown PO. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 2001, 28:327-334. 10.1038/ng569, 11455386.
45. Tornow J, Zeng X, Santangelo GM. GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without DNA binding domain. EMBO J 1993, 12:2431-2437. 413478, 8508768.
46. Yu EY, Morse RH. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol Cell Biol 1999, 19:5279-5288. 84371, 10409719.
47. Brown JWS, Echeverria M, Qu L-H. Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci 2003, 8:42-49. 10.1016/S1360-1385(02)00007-9, 12523999.
48. Brown JWS, Clark GP, Leader DJ, Simpson CG, Lowe T. Multiple snoRNA gene clusters from Arabidopsis. RNA 2001, 7:1817-1832. 1370220, 11780637.
49. Kruszka K, Barneche F, Guyot R, Ailhas J, Meneau I, Schiffer S, Marchfeler A, Echeverria M. Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by Rnase Z. EMBO J 2003, 22:621-632. 10.1093/emboj/cdg040, 140725, 12554662.
50. Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y, Caizergues-Ferrer M, Bachellerie Y. Seven novel methylation guide small nucleolar RNAs are processed from a common polycystronic transcript by Rat1p and Rnase III in yeast. Mol Cell Biol 1999, 19:1144-1158. 116044, 9891049.
51. Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee ST. A program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res 2005, 33(suppl_2):W262-W266. 10.1093/nar/gki368, 1160129, 15980466.