Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production

MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that collectively regulate the expression of a large number of mRNAs by either promoting destabilization or repressing translation, or both. Therefore, they play a major role in shaping the transcriptomes and proteomes of eukaryotic organisms. Typically, animal miRNAs are produced from long primary transcripts with one or more of hairpin structures by two sequential processing reactions: one by Drosha in the nucleus and the other by Dicer in the cytoplasm. However, deviations from this paradigm have been observed: subclasses of miRNAs, which only partially meet the classical definition of a miRNA, are derived by alternative biogenesis pathways, thereby providing an additional level of complexity to miRNA-dependent regulation of gene expression.

[1]  D. Haussecker,et al.  Human tRNA-derived small RNAs in the global regulation of RNA silencing. , 2010, RNA.

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

[3]  A. Hüttenhofer,et al.  The principles of guiding by RNA: chimeric RNA–protein enzymes , 2006, Nature Reviews Genetics.

[4]  N. Rajewsky,et al.  Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.

[5]  Deepak Srivastava,et al.  miR-145 and miR-143 Regulate Smooth Muscle Cell Fate Decisions , 2009, Nature.

[6]  Kuniaki Saito,et al.  Endo‐siRNAs depend on a new isoform of loquacious and target artificially introduced, high‐copy sequences , 2009, The EMBO journal.

[7]  Olivier Voinnet,et al.  Revisiting the principles of microRNA target recognition and mode of action , 2009, Nature Reviews Molecular Cell Biology.

[8]  M. Siomi,et al.  Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. , 2008, Nucleic acids symposium series.

[9]  Geoffrey J. Barton,et al.  Human miRNA Precursors with Box H/ACA snoRNA Features , 2009, PLoS Comput. Biol..

[10]  D. Barford,et al.  Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex , 2005, Nature.

[11]  J. Mattick,et al.  Small RNAs derived from snoRNAs. , 2009, RNA.

[12]  G. Barton,et al.  Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. , 2009, RNA.

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

[14]  Phillip D Zamore,et al.  The RNA-Induced Silencing Complex Is a Mg2+-Dependent Endonuclease , 2004, Current Biology.

[15]  W. Filipowicz,et al.  Relief of microRNA-Mediated Translational Repression in Human Cells Subjected to Stress , 2006, Cell.

[16]  Mikiko C. Siomi,et al.  The Discovery of Rna Interference (rnai) Biogenesis of Small Rnas on the Road to Reading the Rna-interference Code Insight Review , 2022 .

[17]  Eugene Berezikov,et al.  Mammalian mirtron genes. , 2007, Molecular cell.

[18]  Xuemei Chen,et al.  Small RNAs and their roles in plant development. , 2009, Annual review of cell and developmental biology.

[19]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[20]  J. Steitz,et al.  Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation , 2007, Science.

[21]  N. Rajewsky,et al.  A human snoRNA with microRNA-like functions. , 2008, Molecular cell.

[22]  E. Lai,et al.  The Mirtron Pathway Generates microRNA-Class Regulatory RNAs in Drosophila , 2007, Cell.

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

[24]  C. Croce,et al.  MicroRNAs in Cancer. , 2009, Annual review of medicine.

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

[26]  Z. Weng,et al.  Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. , 2010, RNA.

[27]  Gane Ka-Shu Wong,et al.  Minimal introns are not "junk". , 2002, Genome research.

[28]  W. Filipowicz,et al.  Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? , 2008, Nature Reviews Genetics.

[29]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

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

[31]  Satoshi Shibata,et al.  A High-Resolution Structure of the Pre-microRNA Nuclear Export Machinery , 2009, Science.

[32]  I. MacRae,et al.  The RNA-induced Silencing Complex: A Versatile Gene-silencing Machine* , 2009, The Journal of Biological Chemistry.

[33]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[34]  N. Perrimon,et al.  Loquacious isoform endo-siRNAs depends on a specific Drosophila Processing of Material Supplemental , 2009 .

[35]  A. Sandelin,et al.  Hidden layers of human small RNAs , 2008, BMC Genomics.

[36]  E. Lund,et al.  Proofreading and aminoacylation of tRNAs before export from the nucleus. , 1998, Science.

[37]  V. Kim,et al.  Processing of intronic microRNAs , 2007, The EMBO journal.

[38]  A. Marchfelder,et al.  tRNA 3' processing in plants: nuclear and mitochondrial activities differ. , 2000, Biochemistry.

[39]  Tsung-Cheng Chang,et al.  microRNAs in vertebrate physiology and human disease. , 2007, Annual review of genomics and human genetics (Print).

[40]  Lan Jin,et al.  Biological basis for restriction of microRNA targets to the 3' untranslated region in mammalian mRNAs. , 2009, Nature structural & molecular biology.

[41]  Jennifer A. Doudna,et al.  Structural insights into RNA Processing by the Human RISC-Loading Complex , 2009, Nature Structural &Molecular Biology.

[42]  A. Weiner,et al.  E Pluribus Unum: 3' end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs. , 2005, Molecular cell.

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

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

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

[46]  D. Bartel,et al.  Intronic microRNA precursors that bypass Drosha processing , 2007, Nature.

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

[48]  C. Burge,et al.  A computational analysis of sequence features involved in recognition of short introns , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[49]  E. Lai,et al.  Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. , 2009, Molecular cell.

[50]  David W. Taylor,et al.  A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity , 2010, Science.

[51]  G. Hannon,et al.  Crystal Structure of Argonaute and Its Implications for RISC Slicer Activity , 2004, Science.

[52]  V. Kim,et al.  Biogenesis of small RNAs in animals , 2009, Nature Reviews Molecular Cell Biology.

[53]  Hong Duan,et al.  The regulatory activity of microRNA* species has substantial influence on microRNA and 3′ UTR evolution , 2008, Nature Structural &Molecular Biology.

[54]  R. Terns,et al.  Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs , 2007, Nature Reviews Molecular Cell Biology.

[55]  Eric C. Lai,et al.  Endogenous small interfering RNAs in animals , 2008, Nature Reviews Molecular Cell Biology.

[56]  S. Altman.  The road to RNase P , 2000, Nature Structural Biology.

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

[58]  Martin J. Simard,et al.  Argonaute proteins: key players in RNA silencing , 2008, Nature Reviews Molecular Cell Biology.

[59]  G. Hannon,et al.  A dicer-independent miRNA biogenesis pathway that requires Ago catalysis , 2010, Nature.

[60]  Evolutionary biology: Small regulatory RNAs pitch in , 2008, Nature.

[61]  N. Perrimon,et al.  Hierarchical rules for Argonaute loading in Drosophila. , 2009, Molecular cell.

[62]  David P. Bartel,et al.  Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals , 2008, Nature.

[63]  Phillip D. Zamore,et al.  Sorting of Drosophila Small Silencing RNAs , 2007, Cell.

[64]  M. Siomi,et al.  Posttranscriptional regulation of microRNA biogenesis in animals. , 2010, Molecular cell.

[65]  Thomas Tuschl,et al.  Structural basis for 5'-end-specific recognition of the guide RNA strand by the A. fulgidus PIWI protein , 2005 .

[66]  B. Cullen,et al.  A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. , 2010, Molecular cell.

[67]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[68]  Ashesh A. Saraiya,et al.  snoRNA, a Novel Precursor of microRNA in Giardia lamblia , 2008, PLoS pathogens.

[69]  A. Malhotra,et al.  A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). , 2009, Genes & development.

[70]  P. Khaitovich,et al.  Sequence features associated with microRNA strand selection in humans and flies , 2009, BMC Genomics.

[71]  Eugene Berezikov,et al.  Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. , 2006, Genome research.

[72]  E. Mardis.  The impact of next-generation sequencing technology on genetics. , 2008, Trends in genetics : TIG.

[73]  J. Parker.  How to slice: snapshots of Argonaute in action , 2010, Silence.

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

[75]  Robert Blelloch,et al.  Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. , 2008, Genes & development.

[76]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

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

[78]  Anton J. Enright,et al.  Identification of Virus-Encoded MicroRNAs , 2004, Science.

[79]  Hervé Seitz,et al.  Argonaute Loading Improves the 5′ Precision of Both MicroRNAs and Their miRNA∗ Strands in Flies , 2008, Current Biology.

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

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

[82]  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.

[83]  S. Cohen,et al.  microRNA functions. , 2007, Annual review of cell and developmental biology.

[84]  M. Siomi,et al.  Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila. , 2010, RNA.