MicroRNAs: small RNAs with a big role in gene regulation

MicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner. The two founding members of the microRNA family were originally identified in Caenorhabditis elegans as genes that were required for the timed regulation of developmental events. Since then, hundreds of microRNAs have been identified in almost all metazoan genomes, including worms, flies, plants and mammals. MicroRNAs have diverse expression patterns and might regulate various developmental and physiological processes. Their discovery adds a new dimension to our understanding of complex gene regulatory networks.

[1]  Martin Chalfie,et al.  Mutations that lead to reiterations in the cell lineages of C. elegans , 1981, Cell.

[2]  H. Horvitz,et al.  Heterochronic mutants of the nematode Caenorhabditis elegans. , 1984, Science.

[3]  V. Ambros.  A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans , 1989, Cell.

[4]  Gary Ruvkun,et al.  The Caenorhabditis elegans heterochronic gene lin-14 encodes a nuclear protein that forms a temporal developmental switch , 1989, Nature.

[5]  G. Ruvkun,et al.  Negative regulatory sequences in the lin-14 3'-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. , 1991, Genes & development.

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

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

[8]  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.

[9]  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.

[10]  G. Jürgens,et al.  Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis , 1998, The EMBO journal.

[11]  Haifan Lin,et al.  A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. , 1998, Genes & development.

[12]  D. Baulcombe.  Viruses and gene silencing in plants. , 1999, Archives of virology. Supplementum.

[13]  R. Plasterk,et al.  mut-7 of C. elegans, Required for Transposon Silencing and RNA Interference, Is a Homolog of Werner Syndrome Helicase and RNaseD , 1999, Cell.

[14]  Andrew Fire,et al.  The rde-1 Gene, RNA Interference, and Transposon Silencing in C. elegans , 1999, Cell.

[15]  V. Ambros,et al.  The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. , 1999, Developmental biology.

[16]  Phillip D. Zamore,et al.  RNA Interference , 2000, Science.

[17]  P. Sharp,et al.  RNAi Double-Stranded RNA Directs the ATP-Dependent Cleavage of mRNA at 21 to 23 Nucleotide Intervals , 2000, Cell.

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

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

[20]  G. del Solar,et al.  Plasmid copy number control: an ever‐growing story , 2000, Molecular microbiology.

[21]  B. Panning,et al.  X inactivation: Tsix and Xist as yin and yang , 2000, Current Biology.

[22]  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.

[23]  M. Matzke,et al.  Transcriptional silencing and promoter methylation triggered by double‐stranded RNA , 2000, The EMBO journal.

[24]  T. Tuschl,et al.  RNA interference is mediated by 21- and 22-nucleotide RNAs. , 2001, Genes & development.

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

[26]  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.

[27]  B. Bass,et al.  A Role for the RNase III Enzyme DCR-1 in RNA Interference and Germ Line Development in Caenorhabditis elegans , 2001, Science.

[28]  G. Hannon,et al.  C . elegans involved in developmental timing in Dicer functions in RNA interference and in synthesis of small RNA , 2001 .

[29]  D. Court,et al.  Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. , 2001, Structure.

[30]  A. Caudy,et al.  Argonaute2, a Link Between Genetic and Biochemical Analyses of RNAi , 2001, Science.

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

[32]  A. Pasquinelli,et al.  Genes and Mechanisms Related to RNA Interference Regulate Expression of the Small Temporal RNAs that Control C. elegans Developmental Timing , 2001, Cell.

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

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

[35]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[36]  M. Matzke,et al.  RNA-directed DNA methylation in Arabidopsis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

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

[38]  M. Mann,et al.  miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. , 2002, Genes & development.

[39]  C. Croce,et al.  Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Michael Q. Zhang,et al.  The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. , 2002, Genes & development.

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

[42]  Animesh Ray,et al.  DICER-LIKE1: blind men and elephants in Arabidopsis development. , 2002, Trends in plant science.

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

[44]  S. Cohen,et al.  The bantam gene regulates Drosophila growth. , 2002, Genetics.

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

[46]  A. Caudy,et al.  Fragile X-related protein and VIG associate with the RNA interference machinery. , 2002, Genes & development.

[47]  Ira M. Hall,et al.  Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi , 2002, Science.

[48]  B. Reinhart,et al.  MicroRNAs in plants. , 2002, Genes & development.

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

[50]  L. Timmons.  The long and short of siRNAs. , 2002, Molecular cell.

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

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

[53]  B. Cullen,et al.  Sequence requirements for micro RNA processing and function in human cells. , 2003, RNA.

[54]  Gary Ruvkun,et al.  Identification of many microRNAs that copurify with polyribosomes in mammalian neurons , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[55]  E. Sontheimer,et al.  R2D2 Leads the Silencing Trigger to mRNA's Death Star , 2003, Cell.

[56]  Ji-Joon Song,et al.  The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes , 2003, Nature Structural Biology.

[57]  S. Jayasena,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

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

[59]  Marjori Matzke,et al.  Evidence for Nuclear Processing of Plant Micro RNA and Short Interfering RNA Precursors1[w] , 2003, Plant Physiology.

[60]  Ming-Ming Zhou,et al.  Structure and conserved RNA binding of the PAZ domain , 2003, Nature.

[61]  Xiaodong Wang,et al.  R2D2, a Bridge Between the Initiation and Effector Steps of the Drosophila RNAi Pathway , 2003, Science.

[62]  J. Bowman,et al.  Radial Patterning of Arabidopsis Shoots by Class III HD-ZIP and KANADI Genes , 2003, Current Biology.

[63]  V. Ambros,et al.  Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation , 2004, Genome Biology.

[64]  B. Simon,et al.  Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain , 2003, Nature.

[65]  Konstantin Khrapko,et al.  A microRNA array reveals extensive regulation of microRNAs during brain development. , 2003, RNA.

[66]  Michael Z Michael,et al.  Reduced accumulation of specific microRNAs in colorectal neoplasia. , 2003, Molecular cancer research : MCR.

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

[68]  A. Caudy,et al.  A micrococcal nuclease homologue in RNAi effector complexes , 2003, Nature.

[69]  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.

[70]  S. Elledge,et al.  Dicer is essential for mouse development , 2003, Nature Genetics.

[71]  D. Moazed,et al.  Heterochromatin and Epigenetic Control of Gene Expression , 2003, Science.

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

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

[74]  T. Du,et al.  Asymmetry in the Assembly of the RNAi Enzyme Complex , 2003, Cell.

[75]  G. Dreyfuss,et al.  Numerous microRNPs in neuronal cells containing novel microRNAs. , 2003, RNA.

[76]  C. Burge,et al.  Vertebrate MicroRNA Genes , 2003, Science.

[77]  Edwin Cuppen,et al.  The microRNA-producing enzyme Dicer1 is essential for zebrafish development , 2003, Nature Genetics.

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

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

[80]  P. Sharp,et al.  Embryonic stem cell-specific MicroRNAs. , 2003, Developmental cell.

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

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

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

[84]  C. Burge,et al.  Prediction of Mammalian MicroRNA Targets , 2003, Cell.

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

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

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

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

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

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

[91]  S. Hake.  MicroRNAs: A Role in Plant Development , 2003, Current Biology.

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

[93]  C. Croce,et al.  Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

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

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

[96]  E. Sontheimer,et al.  Distinct Roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA Silencing Pathways , 2004, Cell.

[97]  U. Kutay,et al.  Nuclear Export of MicroRNA Precursors , 2004, Science.

[98]  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.

[99]  G. Hannon,et al.  RNase III enzymes and the initiation of gene silencing , 2004, Nature Structural &Molecular Biology.

[100]  Daniela C. Zarnescu,et al.  Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway , 2004, Nature Neuroscience.

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

[102]  Michelle T. Juarez,et al.  microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity , 2004, Nature.

[103]  D. Bartel,et al.  MicroRNA-Directed Cleavage of HOXB8 mRNA , 2004, Science.

[104]  Arndt Borkhardt,et al.  High expression of precursor microRNA‐155/BIC RNA in children with Burkitt lymphoma , 2004, Genes, chromosomes & cancer.

[105]  E. Sontheimer,et al.  A Dicer-2-Dependent 80S Complex Cleaves Targeted mRNAs during RNAi in Drosophila , 2004, Cell.