Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs

Bioinformatics

Volumn 22, Issue 21, 2006, Pages 2585-2589

  Wang, Yu ^a   Hindemitt, Tobias ^a   Mayer, Klaus F X ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA; RNA PRECURSOR;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENE DUPLICATION; GENE TARGETING; GENETIC CONSERVATION; GENETIC REGULATION; GENETIC SIMILARITY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT MODEL; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SEQUENCE ANALYSIS;

ARABIDOPSIS THALIANA;

EID: 33750426743     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl437     Document Type: Article

References (19)

1. Allen,E. et al. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet., 36, 1282-1290.
2. Axtell,M.J. and Bartel,D.P. (2005) Antiquity of MicroRNAs and Their Targets in Land Plants. Plant Cell, 17, 1658-1673.
3. Bartel,D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
4. Baulcombe,D. (2005) RNA silencing. Trends Biochem. Sci., 30, 290-293.
5. Bonnet,E. et al. (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl Acad. Sci. USA, 101, 11511-11516.
6. Griffiths-Jones,S. et al. (2006) miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140-D144.
7. Gustafson,A.M. et al. (2005) ASRP: The Arabidopsis Small RNA Project Database. Nucleic Acids Res., 33, D637-D640.
8. Haberer,G. et al. (2004) Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol, 136, 3009-3022.
9. Hindemitt,T. and Mayer,K. (2005) CREDO: A web-based tool for computational detection of conserved sequence motifs in noncoding sequences. Bioinformatics, 21, 4304-4306.
10. Hurles,M. (2004) Gene duplication: The genomic trade in spare parts. PLoS Biol., 2, E206.
11. Jones-Rhoades,M.W. and Bartel,D.P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell, 14, 787-799.
12. Kurihara,Y. and Watanabe,Y. (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl Acad. Sci. USA, 101, 12753-12758.
13. Lee,Y. et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. Embo J., 23, 4051-4060.
14. Llave,C. et al. (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053-2056.
15. Morgenstern,B. (2004) DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res., 32, W33-36.
16. Schoof,H. et al. (2002) MIPS Arabidopsis thaliana database (MAtDB): An integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res., 30, 91-93.
17. Thijs,G. et al. (2001) A higher order background model improves the detection of regulatory elements by Gibbs sampling. Bioinformatics, 17, 1113-1122.
18. Wang,X.J. et al. (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol., 5, R65.
19. Xie,Z. et al. (2005) Expression of Arabidopsis MIRNA Genes. Plant Physiol, 138, 2145-2154.