Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: Evolutionary footprints of RNA silencing

Molecular BioSystems

Volumn 5, Issue 12, 2009, Pages 1679-1687

  Feng, Jian ^a   Naiman, Daniel Q ^a   Cooper, Bret ^b  

^a Johns Hopkins University   (Ireland)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SPACER DNA;

ARABIDOPSIS; ARTICLE; CHEMISTRY; CHROMOSOME MAP; DNA SEQUENCE; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLANT GENOME; REGULATORY SEQUENCE; RNA INTERFERENCE;

ARABIDOPSIS; BASE SEQUENCE; CHROMOSOME MAPPING; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENOME, HUMAN; GENOME, PLANT; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA INTERFERENCE; SEQUENCE ANALYSIS, DNA;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 72949087527     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/b903031j     Document Type: Article

References (36)

1. T. J. Kelly, Jr H. O. Smith A restriction enzyme from Hemophilus influenzae. II J. Mol. Biol. 1970 51 2 393 409
2. Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome Nature 2005 437 7055 69 87
3. T. Itoh T. Tanaka R. A. Barrero C. Yamasaki Y. Fujii P. B. Hilton B. A. Antonio H. Aono R. Apweiler R. Bruskiewich T. Bureau F. Burr A. Costa de Oliveira G. Fuks T. Habara G. Haberer B. Han E. Harada A. T. Hiraki H. Hirochika D. Hoen H. Hokari S. Hosokawa Y. I. Hsing H. Ikawa K. Ikeo T. Imanishi Y. Ito P. Jaiswal M. Kanno Y. Kawahara T. Kawamura H. Kawashima J. P. Khurana S. Kikuchi S. Komatsu K. O. Koyanagi H. Kubooka D. Lieberherr Y. C. Lin D. Lonsdale T. Matsumoto A. Matsuya W. R. McCombie J. Messing A. Miyao N. Mulder Y. Nagamura J. Nam N. Namiki H. Numa S. Nurimoto C. O'Donovan H. Ohyanagi T. Okido S. Oota N. Osato L. E. Palmer F. Quetier S. Raghuvanshi N. Saichi H. Sakai Y. Sakai K. Sakata T. Sakurai F. Sato Y. Sato H. Schoof M. Seki M. Shibata Y. Shimizu K. Shinozaki Y. Shinso N. K. Singh B. Smith-White J. Takeda M. Tanino T. Tatusova S. Thongjuea F. Todokoro M. Tsugane A. K. Tyagi A. Vanavichit A. Wang R. A. Wing K. Yamaguchi M. Yamamoto N. Yamamoto Y. Yu H. Zhang Q. Zhao K. Higo B. Burr T. Gojobori T. Sasaki Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana Genome Res. 2007 17 2 175 183
4. M. Kellis N. Patterson M. Endrizzi B. Birren E. S. Lander Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003 423 6937 241 254
5. U. Bonas H. Sommer H. Saedler The 17-kb Tam1 element of Antirrhinum majus induces a 3-bp duplication upon integration into the chalcone synthase gene EMBO J. 1984 3 5 1015 1019
6. N. Fedoroff S. Wessler M. Shure Isolation of the transposable maize controlling elements Ac and Ds Cell 1983 35 1 235 242
7. D. L. Hartl Molecular melodies in high and low C Nat. Rev. Genet. 2000 1 2 145 149
8. B. S. Gaut J. Ross-Ibarra Selection on major components of angiosperm genomes Science 2008 320 5875 484 486
9. I. Rigoutsos T. Huynh K. Miranda A. Tsirigos A. McHardy D. Platt Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes Proc. Natl. Acad. Sci. U. S. A. 2006 103 17 6605 6610
10. H. Vaucheret Post-transcriptional small RNA pathways in plants: mechanisms and regulations Genes Dev. 2006 20 7 759 771
11. A. T. Willingham T. R. Gingeras TUF love for "junk" DNA Cell 2006 125 7 1215 1220
12. M. Morgante Plant genome organisation and diversity: the year of the junk! Curr. Opin. Biotechnol. 2006 17 2 168 173
13. T. A. G. Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 2000 408 6814 796 815
14. J. Feng D. Q. Naiman B. Cooper Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies Bioinformatics 2007 23 17 2210 2217
15. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium, The complete sequence of a heterochromatic island from a higher eukaryote Cell 2000 100 3 377 386
16. P. F. Fransz S. Armstrong J. H. de Jong L. D. Parnell C. van Drunen C. Dean P. Zabel T. Bisseling G. H. Jones Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region Cell 2000 100 3 367 376
17. A. Meynert E. Birney Picking pyknons out of the human genome Cell 2006 125 5 836 838
18. J. Jurka Repbase update: a database and an electronic journal of repetitive elements Trends Genet. 2000 16 9 418 420
19. J. M. McAbee T. A. Hill D. J. Skinner A. Izhaki B. A. Hauser R. J. Meister G. Venugopala Reddy E. M. Meyerowitz J. L. Bowman C. S. Gasser ABERRANT TESTA SHAPE encodes a KANADI family member, linking polarity determination to separation and growth of Arabidopsis ovule integuments Plant J. 2006 46 3 522 531
20. D. Baulcombe RNA silencing in plants Nature 2004 431 7006 356 363
21. D. P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 2004 116 2 281 297
22. K. D. Kasschau N. Fahlgren E. J. Chapman C. M. Sullivan J. S. Cumbie S. A. Givan J. C. Carrington Genome-wide profiling and analysis of Arabidopsis siRNAs PLoS Biol. 2007 5 3 e57
23. A. M. Gustafson E. Allen S. Givan D. Smith J. C. Carrington K. D. Kasschau ASRP: the Arabidopsis Small RNA Project Database Nucleic Acids Res. 2005 33 Database Issue D637 640
24. S. W. Ding O. Voinnet Antiviral immunity directed by small RNAs Cell 2007 130 3 413 426
25. T. Watanabe Y. Totoki A. Toyoda M. Kaneda S. Kuramochi-Miyagawa Y. Obata H. Chiba Y. Kohara T. Kono T. Nakano M. A. Surani Y. Sakaki H. Sasaki Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes Nature 2008 453 7194 539 543
26. D. Zilberman S. Henikoff Silencing of transposons in plant genomes; kick them when they're down Genome Biol. 2004 5 12 249
27. E. Bernstein C. D. Allis RNA meets chromatin Genes Dev. 2005 19 14 1635 1655
28. S. W. Chan I. R. Henderson S. E. Jacobsen Gardening the genome: DNA methylation in Arabidopsis thaliana Nat. Rev. Genet. 2005 6 5 351 360
29. S. Boi G. Solda M. L. Tenchini Shedding light on the dark side of the genome; overlapping genes in higher eukaryotes Curr. Genomics 2004 5509 524
30. C. H. Jen I. Michalopoulos D. R. Westhead P. Meyer Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation Genome Biol. 2005 6 6 R51
31. K. Yamada J. Lim J. M. Dale H. Chen P. Shinn C. J. Palm A. M. Southwick H. C. Wu C. Kim M. Nguyen P. Pham R. Cheuk G. Karlin-Newmann S. X. Liu B. Lam H. Sakano T. Wu G. Yu M. Miranda H. L. Quach M. Tripp C. H. Chang J. M. Lee M. Toriumi M. M. Chan C. C. Tang C. S. Onodera J. M. Deng K. Akiyama Y. Ansari T. Arakawa J. Banh F. Banno L. Bowser S. Brooks P. Carninci Q. Chao N. Choy A. Enju A. D. Goldsmith M. Gurjal N. F. Hansen Y. Hayashizaki C. Johnson-Hopson V. W. Hsuan K. Iida M. Karnes S. Khan E. Koesema J. Ishida P. X. Jiang T. Jones J. Kawai A. Kamiya C. Meyers M. Nakajima M. Narusaka M. Seki T. Sakurai M. Satou R. Tamse M. Vaysberg E. K. Wallender C. Wong Y. Yamamura S. Yuan K. Shinozaki R. W. Davis A. Theologis J. R. Ecker Empirical analysis of transcriptional activity in the Arabidopsis genome Science 2003 302 5646 842 846
32. M. J. Axtell C. Jan R. Rajagopalan D. P. Bartel A two-hit trigger for siRNA biogenesis in plants Cell 2006 127 3 565 577
33. J. Pak A. Fire Distinct populations of primary and secondary effectors during RNAi in C. elegans Science 2007 315 5809 241 244
34. N. Jiang Z. Bao X. Zhang S. R. Eddy S. R. Wessler Pack-MULE transposable elements mediate gene evolution in plants Nature 2004 431 7008 569 573
35. J. S. Mattick I. V. Makunin Non-coding RNA Hum. Mol. Genet. 2006 15 Review Issue 1 R17 29
36. E. K. Round S. K. Flowers E. J. Richards Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure Genome Res. 1997 7 11 1045 1053