A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans

[1]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

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

[3]  R. Russell,et al.  Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution , 2005, Cell.

[4]  Olivier Elemento,et al.  Revealing Posttranscriptional Regulatory Elements Through Network-Level Conservation , 2005, PLoS Comput. Biol..

[5]  Ligang Wu,et al.  Micro-RNA Regulation of the Mammalian lin-28 Gene during Neuronal Differentiation of Embryonal Carcinoma Cells , 2005, Molecular and Cellular Biology.

[6]  Michael Q. Zhang,et al.  Regulating Gene Expression through RNA Nuclear Retention , 2005, Cell.

[7]  Zuoren Yu,et al.  MicroRNA Mirn122a Reduces Expression of the Posttranscriptionally Regulated Germ Cell Transition Protein 2 (Tnp2) Messenger RNA (mRNA) by mRNA Cleavage1 , 2005, Biology of reproduction.

[8]  H. Horvitz,et al.  The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. , 2005, Developmental cell.

[9]  Marc Vidal,et al.  Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis , 2005, Nature.

[10]  T. Tuschl,et al.  Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. , 2005, Molecular cell.

[11]  Yong Zhao,et al.  Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis , 2005, Nature.

[12]  Debora S. Marks,et al.  Antisense-Mediated Depletion Reveals Essential and Specific Functions of MicroRNAs in Drosophila Development , 2005, Cell.

[13]  Kathryn A. O’Donnell,et al.  c-Myc-regulated microRNAs modulate E2F1 expression , 2005, Nature.

[14]  S. Lowe,et al.  A microRNA polycistron as a potential human oncogene , 2005, Nature.

[15]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[16]  Kristin C. Gunsalus,et al.  microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets , 2005, PLoS Comput. Biol..

[17]  Anton J. Enright,et al.  Materials and Methods Figs. S1 to S4 Tables S1 to S5 References and Notes Micrornas Regulate Brain Morphogenesis in Zebrafish , 2022 .

[18]  Gerald M Rubin,et al.  Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. , 2005, Genes & development.

[19]  James R. Brown,et al.  A computational view of microRNAs and their targets. , 2005, Drug discovery today.

[20]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[21]  Marvin Wickens,et al.  Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1. , 2005, RNA.

[22]  Thomas Tuschl,et al.  Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein , 2005, Nature.

[23]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[24]  Y. Li,et al.  Incorporating structure to predict microRNA targets. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[25]  F. Slack,et al.  RAS Is Regulated by the let-7 MicroRNA Family , 2005, Cell.

[26]  Mark Gerstein,et al.  The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. , 2005, Developmental cell.

[27]  R. Russell,et al.  Principles of MicroRNA–Target Recognition , 2005, PLoS biology.

[28]  F. Slack,et al.  Developmental timing in C. elegans is regulated by kin-20 and tim-1, homologs of core circadian clock genes. , 2005, Developmental cell.

[29]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[30]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[31]  Kimberly Van Auken,et al.  WormBase: a comprehensive data resource for Caenorhabditis biology and genomics , 2004, Nucleic Acids Res..

[32]  M. Kiriakidou,et al.  Detection of microRNAs and assays to monitor microRNA activities in vivo and in vitro. , 2005, Methods in molecular biology.

[33]  P. Macdonald,et al.  Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method , 2005, BMC Genomics.

[34]  Ravi Jain,et al.  MicroRNA-143 Regulates Adipocyte Differentiation* , 2004, Journal of Biological Chemistry.

[35]  F. Slack,et al.  Architecture of a validated microRNA::target interaction. , 2004, Chemistry & biology.

[36]  N. Rajewsky,et al.  A pancreatic islet-specific microRNA regulates insulin secretion , 2004, Nature.

[37]  David E Hill,et al.  A first version of the Caenorhabditis elegans Promoterome. , 2004, Genome research.

[38]  Oliver Hobert,et al.  MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode , 2004, Nature.

[39]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature Reviews Genetics.

[40]  Fabio Piano,et al.  Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[42]  John G Doench,et al.  Specificity of microRNA target selection in translational repression. , 2004, Genes & development.

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

[44]  Eun-Young Choi,et al.  The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. , 2004, Genes & development.

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

[46]  D. Bartel,et al.  MicroRNAs Modulate Hematopoietic Lineage Differentiation , 2004, Science.

[47]  Lior Pachter,et al.  MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.

[48]  Kristin C. Gunsalus,et al.  RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects , 2004, Nucleic Acids Res..

[49]  Oliver Hobert,et al.  A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans , 2003, Nature.

[50]  Chris Sander,et al.  Characterizing gene sets with FuncAssociate , 2003, Bioinform..

[51]  R. Durbin,et al.  The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics , 2003, PLoS biology.

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

[53]  R. Kamath,et al.  Genome-wide RNAi screening in Caenorhabditis elegans. , 2003, Methods.

[54]  F. Slack,et al.  The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. , 2003, Developmental biology.

[55]  K. Taira,et al.  Hes1 is a target of microRNA-23 during retinoic-acid-induced neuronal differentiation of NT2 cells , 2003, Nature.

[56]  V. Ambros,et al.  MicroRNAs and Other Tiny Endogenous RNAs in C. elegans , 2003, Current Biology.

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

[58]  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.

[59]  Daniel L. Hartl,et al.  GeneMerge - Post-genomic Analysis, Data Mining, and Hypothesis Testing , 2003, Bioinform..

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

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

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

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

[64]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[65]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[66]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[67]  E. Lai.  Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation , 2002, Nature Genetics.

[68]  V. Ambros,et al.  An Extensive Class of Small RNAs in Caenorhabditis elegans , 2001, Science.

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

[70]  Ian Korf,et al.  Integrating genomic homology into gene structure prediction , 2001, ISMB.

[71]  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.

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

[73]  V. Ambros,et al.  The timing of lin-4 RNA accumulation controls the timing of postembryonic developmental events in Caenorhabditis elegans. , 1999, Developmental biology.

[74]  J. Culotti,et al.  Pioneer axon guidance by UNC-129, a C. elegans TGF-beta. , 1998, Science.

[75]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[76]  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.

[77]  G. Ruvkun,et al.  A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. , 1996, Genes & development.

[78]  D. Albertson,et al.  Expression patterns of predicted genes from the C. elegans genome sequence visualized by FISH in whole organisms , 1995, Nature Genetics.

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

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

[81]  AC Tose.  Cell , 1993, Cell.

[82]  Temple F. Smith,et al.  Prediction of gene structure. , 1992, Journal of molecular biology.

[83]  V. Ambros,et al.  Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences. , 1991, The EMBO journal.