Computational detection of microRNAs targeting transcription factor genes in Arabidopsis thaliana

MicroRNAs, an abundant class of tiny non-coding RNAs, have emerged as negative regulators for translational repression or cleavage of target mRNAs by the manner of complementary base paring in plants and animals. Recent studies have demonstrated that many known microRNAs have a remarkable propensity to target genes involved in development, particularly those of transcription factor genes. Therefore, an overall detection of Arabidopsis thaliana microRNAs targeting transcription factor genes will enhance greatly our understanding of microRNA biological functions in plant development. By searching short complementary sequences between transcription factor open-reading frames and intergenic region sequences, and considering RNA secondary structures and the sequence conversation between the genomes of Arabidopsis and Oryza sativa, we detected 96 candidate Arabidopsis microRNAs. These candidate microRNAs were predicted to target 102 transcription factor genes that are classified as 28 transcription factor gene families, particularly those of DNA-binding transcription factor families, which imply that microRNAs might be involved in complex transcriptional regulatory networks for specifying individual cell types in plant development.

[1]  Xuemei Chen,et al.  A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development , 2004, Science.

[2]  E. Davidson.  Genomic Regulatory Systems , 2001 .

[3]  Rupert De Wachter,et al.  RnaViz 2: an improved representation of RNA secondary structure , 2003, Bioinform..

[4]  David P. Bartel,et al.  MicroRNAs: At the Root of Plant Development?1 , 2003, Plant Physiology.

[5]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[6]  C. E. SHANNON,et al.  A mathematical theory of communication , 1948, MOCO.

[7]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[8]  D. Bartel,et al.  Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. , 2004, Molecular cell.

[9]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[10]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[11]  P. Rouzé,et al.  Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Eric C Lai,et al.  microRNAs: Runts of the Genome Assert Themselves , 2003, Current Biology.

[13]  E. Huq,et al.  The Arabidopsis Basic/Helix-Loop-Helix Transcription Factor Family Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.013839. , 2003, The Plant Cell Online.

[14]  C. Llave,et al.  Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA , 2002, Science.

[15]  M. Ptashne.  A Genetic Switch , 1986 .

[16]  G. Church,et al.  Computational and experimental identification of C. elegans microRNAs. , 2003, Molecular cell.

[17]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[18]  B. Reinhart,et al.  A biochemical framework for RNA silencing in plants. , 2003, Genes & development.

[19]  Hajime Sakai,et al.  Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016238. , 2003, The Plant Cell Online.

[20]  L. Lim,et al.  An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.

[21]  M. Barton,et al.  MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. , 2004, Developmental cell.

[22]  P. Bailey,et al.  The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. , 2003, Molecular biology and evolution.

[23]  Sanghyuk Lee,et al.  MicroRNA genes are transcribed by RNA polymerase II , 2004, The EMBO journal.

[24]  G. Rubin,et al.  Computational identification of Drosophila microRNA genes , 2003, Genome Biology.

[25]  M. A. Rector,et al.  Endogenous and Silencing-Associated Small RNAs in Plants Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.003210. , 2002, The Plant Cell Online.

[26]  Terry Gaasterland,et al.  Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets , 2004, Genome Biology.

[27]  V. Ambros,et al.  Role of MicroRNAs in Plant and Animal Development , 2003, Science.

[28]  B. Reinhart,et al.  Prediction of Plant MicroRNA Targets , 2002, Cell.

[29]  C. Kidner,et al.  The developmental role of microRNA in plants. , 2005, Current opinion in plant biology.

[30]  V. Kim,et al.  The nuclear RNase III Drosha initiates microRNA processing , 2003, Nature.

[31]  C. Burge,et al.  The microRNAs of Caenorhabditis elegans. , 2003, Genes & development.