Principles of micro-RNA production and maturation

Micro-RNAs (miRNAs) are a class of approximately 22-nucleotide non-coding RNAs expressed in multicellular organisms. They are first transcribed in a similar manner to pre-mRNAs. The transcripts then go through a series of processing steps, including endonucleolytic cleavage, nuclear export and a strand selection procedure, to yield the single-stranded mature miRNA products. The transcription and processing of miRNAs determines the abundance and the sequence of mature miRNAs and has important implications for the function of miRNAs.

[1]  Henry Mirsky,et al.  RNA editing of a miRNA precursor. , 2004, RNA.

[2]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[3]  B. Cullen Transcription and processing of human microRNA precursors. , 2004, Molecular cell.

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

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

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

[7]  Z. Mourelatos,et al.  A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. , 2005, Genes & development.

[8]  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.

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

[10]  Qinghua Liu,et al.  Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila. , 2005, Genes & development.

[11]  Gail Mandel,et al.  Reciprocal actions of REST and a microRNA promote neuronal identity , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[12]  D. Patel,et al.  Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain , 2004, Nature.

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

[14]  Eric Westhof,et al.  Single Processing Center Models for Human Dicer and Bacterial RNase III , 2004, Cell.

[15]  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.

[16]  B. Cullen,et al.  Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. , 2003, Genes & development.

[17]  R. Shiekhattar,et al.  TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing , 2005, Nature.

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

[19]  Phillip D Zamore,et al.  microPrimer: the biogenesis and function of microRNA , 2005, Development.

[20]  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.

[21]  K. Czaplinski,et al.  Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. , 2004, RNA.

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

[23]  Angela N. Brooks,et al.  Structural Basis for Double-Stranded RNA Processing by Dicer , 2006, Science.

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

[25]  P. Zamore,et al.  A Protein Sensor for siRNA Asymmetry , 2004, Science.

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

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

[28]  R. Shiekhattar,et al.  The Microprocessor complex mediates the genesis of microRNAs , 2004, Nature.

[29]  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.

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

[31]  W. Tam Identification and characterization of human BIC, a gene on chromosome 21 that encodes a noncoding RNA. , 2001, Gene.

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

[33]  V. Kim,et al.  The role of PACT in the RNA silencing pathway , 2006, The EMBO journal.

[34]  G. L. Eliceiri Small nucleolar RNAs , 1999, Cellular and Molecular Life Sciences CMLS.

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

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

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

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

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

[40]  V. Kim MicroRNA biogenesis: coordinated cropping and dicing , 2005, Nature Reviews Molecular Cell Biology.

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

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

[43]  Guiliang Tang,et al.  MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region , 2004 .

[44]  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.

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

[46]  B. Cullen,et al.  Efficient Processing of Primary microRNA Hairpins by Drosha Requires Flanking Nonstructured RNA Sequences* , 2005, Journal of Biological Chemistry.

[47]  V. Ambros,et al.  Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. , 2005, Genes & development.

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

[49]  Anastasia Khvorova,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

[50]  Byoung-Tak Zhang,et al.  Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex , 2006, Cell.

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

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

[53]  Rudolf Jaenisch,et al.  Characterization of a highly variable eutherian microRNA gene. , 2005, RNA.

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

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

[56]  Edouard Bertrand,et al.  Exportin-5 Mediates Nuclear Export of Minihelix-containing RNAs* , 2003, The Journal of Biological Chemistry.

[57]  B. Cullen,et al.  Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. , 2004, RNA.

[58]  Yuasa Takashi,et al.  The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. , 2005, RNA.

[59]  B. Cullen,et al.  Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha , 2005, The EMBO journal.

[60]  Kazuo Shinozaki,et al.  Specific interactions between Dicer-like proteins and HYL1/DRB- family dsRNA-binding proteins in Arabidopsis thaliana , 2004, Plant Molecular Biology.

[61]  G. Hannon,et al.  Processing of primary microRNAs by the Microprocessor complex , 2004, Nature.

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

[63]  H. Goodman,et al.  Uridine Addition After MicroRNA-Directed Cleavage , 2004, Science.

[64]  J. M. Thomson,et al.  Argonaute2 Is the Catalytic Engine of Mammalian RNAi , 2004, Science.

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

[66]  Gang Wu,et al.  Nuclear processing and export of microRNAs in Arabidopsis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[67]  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.

[68]  W. Filipowicz,et al.  Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP , 2002, The EMBO journal.

[69]  C. Sander,et al.  Identification of microRNAs of the herpesvirus family , 2005, Nature Methods.

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

[71]  John Bracht,et al.  Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. , 2004, RNA.

[72]  A. Denli,et al.  Normal microRNA Maturation and Germ-Line Stem Cell Maintenance Requires Loquacious, a Double-Stranded RNA-Binding Domain Protein , 2005, PLoS biology.

[73]  V. Kim,et al.  The Drosha-DGCR8 complex in primary microRNA processing. , 2004, Genes & development.

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

[75]  W. Filipowicz,et al.  Characterization of the interactions between mammalian PAZ PIWI domain proteins and Dicer , 2004, EMBO reports.

[76]  Xuemei Chen,et al.  Methylation Protects miRNAs and siRNAs from a 3′-End Uridylation Activity in Arabidopsis , 2005, Current Biology.

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

[78]  Alessandro Fatica,et al.  A Minicircuitry Comprised of MicroRNA-223 and Transcription Factors NFI-A and C/EBPα Regulates Human Granulopoiesis , 2005, Cell.

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

[80]  R. Shiekhattar,et al.  Human RISC Couples MicroRNA Biogenesis and Posttranscriptional Gene Silencing , 2005, Cell.

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

[82]  Ben Berkhout,et al.  Suppression of RNA Interference by Adenovirus Virus-Associated RNA , 2005, Journal of Virology.

[83]  Yuichiro Watanabe,et al.  Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Kuniaki Saito,et al.  Processing of Pre-microRNAs by the Dicer-1–Loquacious Complex in Drosophila Cells , 2005, PLoS biology.

[85]  M. Siomi,et al.  A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. , 2002, Genes & development.

[86]  W. Filipowicz,et al.  Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[87]  T. Tuschl,et al.  The Human DiGeorge Syndrome Critical Region Gene 8 and Its D. melanogaster Homolog Are Required for miRNA Biogenesis , 2004, Current Biology.

[88]  Kaoru Saigo,et al.  Short-Interfering-RNA-Mediated Gene Silencing in Mammalian Cells Requires Dicer and eIF2C Translation Initiation Factors , 2003, Current Biology.

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

[90]  Anne Gatignol,et al.  TRBP, a regulator of cellular PKR and HIV‐1 virus expression, interacts with Dicer and functions in RNA silencing , 2005, EMBO reports.

[91]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[92]  Anton J. Enright,et al.  RNA editing of human microRNAs , 2006, Genome Biology.

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

[94]  B. Samuelsson,et al.  Ribonuclease activity and RNA binding of recombinant human Dicer , 2002, The EMBO journal.

[95]  Xuemei Chen,et al.  Methylation as a Crucial Step in Plant microRNA Biogenesis , 2005, Science.