Computational Prediction of Candidate miRNAs and their Targets from Medicago truncatula Non-Protein-Coding Transcripts

Identification and analysis of miRNAs enhances our understanding of the important roles that small RNAs play in complex regulatory networks. It is often difficult to perform large-scale validation of miRNA expression that is predicted from genomic regions. Expressed transcripts provide an alternative resource to facilitate identification of miRNAs and their targets. We developed a computational pipeline to scan for miRNA genes from polyadenylated transcripts that were associated with limited protein coding potentials, corresponding to the intergenic regions of Medicago truncatula genomic sequences. Each predicted miRNA was required to have a near perfect match with target genes. We also searched for miRNA conservation in other plant species, clustered highly similar miRNAs, and provided a functional classification of target genes.

[1]  Andrei N. Lupas,et al.  CLANS: a Java application for visualizing protein families based on pairwise similarity , 2004, Bioinform..

[2]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[3]  A. Bradley,et al.  Identification of mammalian microRNA host genes and transcription units. , 2004, Genome research.

[4]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

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

[6]  J. Bowman,et al.  MicroRNAs: Micro‐managing the Plant Genome , 2007 .

[7]  A. Adai,et al.  Computational prediction of miRNAs in Arabidopsis thaliana. , 2005, Genome research.

[8]  D. Bartel,et al.  Antiquity of MicroRNAs and Their Targets in Land Plantsw⃞ , 2005, The Plant Cell Online.

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

[10]  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.

[11]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[12]  Peter M. Waterhouse,et al.  Plant and animal microRNAs: similarities and differences , 2005, Functional & Integrative Genomics.

[13]  Brian J. Parker,et al.  In Silico Identification and Characterization of mRNA-Like Noncoding Transcripts in Medicago truncatula , 2007, Silico Biol..

[14]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[15]  Jan Krüger,et al.  RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..

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

[17]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[18]  Wen-chang Lin,et al.  Bioinformatic discovery of microRNA precursors from human ESTs and introns , 2006, BMC Genomics.

[19]  Baohong Zhang,et al.  Plant microRNA: a small regulatory molecule with big impact. , 2006, Developmental biology.

[20]  Tobias Dezulian,et al.  Conservation and divergence of microRNA families in plants , 2005, Genome Biology.

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