MicroRNA targets in Drosophila

BackgroundThe recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. We present a computational method for whole-genome prediction of miRNA target genes. The method is validated using known examples. For each miRNA, target genes are selected on the basis of three properties: sequence complementarity using a position-weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Application to the D. melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known miRNAs.ResultsThese potential targets are rich in genes that are expressed at specific developmental stages and that are involved in cell fate specification, morphogenesis and the coordination of developmental processes, as well as genes that are active in the mature nervous system. High-ranking target genes are enriched in transcription factors two-fold and include genes already known to be under translational regulation. Our results reaffirm the thesis that miRNAs have an important role in establishing the complex spatial and temporal patterns of gene activity necessary for the orderly progression of development and suggest additional roles in the function of the mature organism. In addition the results point the way to directed experiments to determine miRNA functions.ConclusionsThe emerging combinatorics of miRNA target sites in the 3' untranslated regions of messenger RNAs are reminiscent of transcriptional regulation in promoter regions of DNA, with both one-to-many and many-to-one relationships between regulator and target. Typically, more than one miRNA regulates one message, indicative of cooperative translational control. Conversely, one miRNA may have several target genes, reflecting target multiplicity. As a guide to focused experiments, we provide detailed online information about likely target genes and binding sites in their untranslated regions, organized by miRNA or by gene and ranked by likelihood of match. The target prediction algorithm is freely available and can be applied to whole genome sequences using identified miRNA sequences.

[1]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[2]  M. Waterman,et al.  A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. , 1987, Journal of molecular biology.

[3]  William McGinnis,et al.  Homeobox genes and axial patterning , 1992, Cell.

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

[5]  G. Ruvkun,et al.  Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans , 1993, Cell.

[6]  M. Bate,et al.  The development of Drosophila melanogaster , 1993 .

[7]  V. Ambros,et al.  Heterochronic genes and the temporal control of C. elegans development. , 1994, Trends in genetics : TIG.

[8]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[9]  R. Mann,et al.  Why are Hox genes clustered? , 1997, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  F. Slack,et al.  Temporal pattern formation by heterochronic genes. , 1997, Annual review of genetics.

[11]  C. Thummel,et al.  Steroid regulated programmed cell death during Drosophila metamorphosis. , 1997, Development.

[12]  Hyung Don Ryoo,et al.  Nuclear Translocation of Extradenticle Requires homothorax , which Encodes an Extradenticle-Related Homeodomain Protein , 1997, Cell.

[13]  Chris Sander,et al.  The HSSP database of protein structure-sequence alignments , 1993, Nucleic Acids Res..

[14]  V. Ambros,et al.  The Cold Shock Domain Protein LIN-28 Controls Developmental Timing in C. elegans and Is Regulated by the lin-4 RNA , 1997, Cell.

[15]  David R. Gilbert,et al.  FlyBase: a Drosophila database. The FlyBase consortium , 1997, Nucleic Acids Res..

[16]  C. Thummel,et al.  crooked legs encodes a family of zinc finger proteins required for leg morphogenesis and ecdysone-regulated gene expression during Drosophila metamorphosis. , 1998, Development.

[17]  M. Akam,et al.  Hox genes: From master genes to micromanagers , 1998, Current Biology.

[18]  C Burks,et al.  The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. , 1998, Development.

[19]  Biological Laboratories Divinity Avenue Cambridge Ma Usa. FlyBase.  FlyBase: a Drosophila database. , 1998, Nucleic acids research.

[20]  Craig T. Woodard,et al.  The Drosophila beta FTZ-F1 orphan nuclear receptor provides competence for stage-specific responses to the steroid hormone ecdysone. , 1999, Molecular cell.

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

[22]  A. J. Schroeder,et al.  The FlyBase database of the Drosophila Genome Projects and community literature. , 2002, Nucleic acids research.

[23]  B. Mueller,et al.  Growth cone guidance: first steps towards a deeper understanding. , 1999, Annual review of neuroscience.

[24]  P. Schuster,et al.  Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.

[25]  Marc Tessier-Lavigne,et al.  Conservation and divergence of axon guidance mechanisms , 1999, Current Opinion in Neurobiology.

[26]  L. Gilbert,et al.  Transcriptional activation of the Drosophila ecdysone receptor by insect and plant ecdysteroids. , 2000, Insect biochemistry and molecular biology.

[27]  S. Hammond,et al.  An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells , 2000, Nature.

[28]  J. Littleton,et al.  Ion Channels and Synaptic Organization Analysis of the Drosophila Genome , 2000, Neuron.

[29]  L. Gilbert,et al.  The mutation without children(rgl) causes ecdysteroid deficiency in third-instar larvae of Drosophila melanogaster. , 2000, Developmental biology.

[30]  Graziano Pesole,et al.  UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs , 2000, Nucleic Acids Res..

[31]  E. Baehrecke,et al.  Steroid regulation of programmed cell death during Drosophila development , 2000, Cell Death and Differentiation.

[32]  B. Reinhart,et al.  The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans , 2000, Nature.

[33]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[34]  B. Reinhart,et al.  Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA , 2000, Nature.

[35]  F. Slack,et al.  The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. , 2000, Molecular cell.

[36]  T. Kadesch,et al.  Notch signaling: a dance of proteins changing partners. , 2000, Experimental cell research.

[37]  C. Thummel,et al.  A steroid-triggered transcriptional hierarchy controls salivary gland cell death during Drosophila metamorphosis. , 2000, Molecular cell.

[38]  P. Chambon,et al.  Bonus, a Drosophila homolog of TIF1 proteins, interacts with nuclear receptors and can inhibit betaFTZ-F1-dependent transcription. , 2001, Molecular cell.

[39]  A. Pasquinelli,et al.  A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA , 2001, Science.

[40]  G. Rubin,et al.  neuralized is essential for a subset of Notch pathway-dependent cell fate decisions during Drosophila eye development , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[41]  C. Thummel,et al.  Molecular mechanisms of developmental timing in C. elegans and Drosophila. , 2001, Developmental cell.

[42]  T. Tuschl,et al.  Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate , 2001, The EMBO journal.

[43]  A. Caudy,et al.  Role for a bidentate ribonuclease in the initiation step of RNA interference , 2001 .

[44]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[45]  T. Tuschl,et al.  Identification of Tissue-Specific MicroRNAs from Mouse , 2002, Current Biology.

[46]  C. Rabouille,et al.  Ecdysone triggers the expression of Golgi genes in Drosophila imaginal discs via broad-complex. , 2002, Developmental biology.

[47]  G. Hutvagner,et al.  A microRNA in a Multiple-Turnover RNAi Enzyme Complex , 2002, Science.

[48]  J. Chory,et al.  Steroid signaling in plants and insects--common themes, different pathways. , 2002, Genes & development.

[49]  J. Messing,et al.  CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thaliana , 2002, Current Biology.

[50]  E. Giniger.  How do Rho family GTPases direct axon growth and guidance? A proposal relating signaling pathways to growth cone mechanics. , 2002, Differentiation; research in biological diversity.

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

[52]  A. Pasquinelli,et al.  Control of developmental timing by micrornas and their targets. , 2002, Annual review of cell and developmental biology.

[53]  A. Pasquinelli,et al.  MicroRNAs: deviants no longer. , 2002, Trends in genetics : TIG.

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

[55]  J. Simon,et al.  Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes. , 2002, Current opinion in genetics & development.

[56]  V. Kim,et al.  MicroRNA maturation: stepwise processing and subcellular localization , 2002, The EMBO journal.

[57]  Michael Ashburner,et al.  On ontologies for biologists: the Gene Ontology--untangling the web. , 2002, Novartis Foundation symposium.

[58]  Graziano Pesole,et al.  UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002 , 2002, Nucleic Acids Res..

[59]  Annick Harel-Bellan,et al.  Synthetic small inhibiting RNAs: Efficient tools to inactivate oncogenic mutations and restore p53 pathways , 2002 .

[60]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[61]  B. Li,et al.  Expression profiling reveals off-target gene regulation by RNAi , 2003, Nature Biotechnology.

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

[63]  V. Ambros.  MicroRNA Pathways in Flies and Worms Growth, Death, Fat, Stress, and Timing , 2003, Cell.

[64]  R. Steward,et al.  Tamo selectively modulates nuclear import in Drosophila , 2003, Genes to cells : devoted to molecular & cellular mechanisms.

[65]  Anindya Dutta,et al.  Small RNAs with Imperfect Match to Endogenous mRNA Repress Translation , 2003, Journal of Biological Chemistry.

[66]  Nicholas L. Bray,et al.  AVID: A global alignment program. , 2003, Genome research.

[67]  S. Choksi,et al.  amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development. , 2003, Genetics.

[68]  T. Tuschl,et al.  New microRNAs from mouse and human. , 2003, RNA.

[69]  E. Moss,et al.  Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites. , 2003, Developmental biology.

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

[71]  A. Rougvie,et al.  The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. , 2003, Developmental cell.

[72]  E. Moss,et al.  Erratum to “Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites”: [Dev. Biol. 258 (2003) 432–442]☆ , 2003 .

[73]  R. Russell,et al.  bantam Encodes a Developmentally Regulated microRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene hid in Drosophila , 2003, Cell.

[74]  D. Marks,et al.  The small RNA profile during Drosophila melanogaster development. , 2003, Developmental cell.

[75]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[76]  The FlyBase database of the Drosophila genome projects and community literature. , 2003, Nucleic acids research.

[77]  Chiara Gamberi,et al.  The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. , 2003, Developmental cell.

[78]  Julius Brennecke,et al.  Identification of Drosophila MicroRNA Targets , 2003, PLoS biology.

[79]  Phillip A Sharp,et al.  siRNAs can function as miRNAs , 2003 .

[80]  Z. Xie,et al.  Negative Feedback Regulation of Dicer-Like1 in Arabidopsis by microRNA-Guided mRNA Degradation , 2003, Current Biology.

[81]  S. Benzer,et al.  Steroid Control of Longevity in Drosophila melanogaster , 2003, Science.

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

[83]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[84]  Javier F. Palatnik,et al.  Control of leaf morphogenesis by microRNAs , 2003, Nature.

[85]  Bruce A. Hay,et al.  The Drosophila MicroRNA Mir-14 Suppresses Cell Death and Is Required for Normal Fat Metabolism , 2003, Current Biology.

[86]  B. Cullen,et al.  MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

[88]  V. Ambros,et al.  Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity. , 2003, Developmental biology.

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

[90]  Neff Walker,et al.  A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development , 2004 .

[91]  Nikolaus Rajewsky,et al.  Computational identification of microRNA targets , 2004, Genome Biology.

[92]  Natalie Wilson,et al.  The miRNA Registry , 2004, Nature Reviews Genetics.