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The Fate of miRNA* Strand through Evolutionary Analysis: Implication for Degradation As Merely Carrier Strand or Potential Regulatory Molecule?

Guo, Li, Lu, Zuhong·2010·PLoS ONE

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  1. [1]Bartel DP 2004 MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116 281 297 14744438
  2. [2]Plasterk RHA 2006 Micro RNAs in animal development. Cell 124 877 881 16530032
  3. [3]Borchert GM Lanier W Davidson BL 2006 RNA polymerase III transcribes human microRNAs. Nature Structural & Molecular Biology 13 1097 1101 17099701
  4. [4]Cai XZ Hagedorn CH Cullen BR 2004 Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. Rna-a Publication of the Rna Society 10 1957 1966 PMC1370684 15525708
  5. [5]Lee Y Kim M Han JJ Yeom KH Lee S 2004 MicroRNA genes are transcribed by RNA polymerase II. Embo Journal 23 4051 4060 15372072 PMC524334
  6. [6]Filipowicz W Bhattacharyya SN Sonenberg N 2008 Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Reviews Genetics 9 102 114 18197166
  7. [7]Friedlander MR Chen W Adamidi C Maaskola J Einspanier R 2008 Discovering microRNAs from deep sequencing data using miRDeep. Nature Biotechnology 26 407 415 18392026
  8. [8]Grishok A Pasquinelli AE Conte D Li N Parrish S 2001 Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C-elegans developmental timing. Cell 106 23 34 11461699
  9. [9]Hutvagner G McLachlan J Pasquinelli AE Balint E Tuschl T 2001 A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293 834 838 11452083
  10. [10]Lund E Guttinger S Calado A Dahlberg JE Kutay U 2004 Nuclear export of microRNA precursors. Science 303 95 98 14631048
  11. [11]Schwarz DS Hutvagner G Du T Xu ZS Aronin N 2003 Asymmetry in the assembly of the RNAi enzyme complex. Cell 115 199 208 14567917
  12. [12]Schwarz DS Hutvagner G Du TT Xu ZS Aronin N 2007 Asymmetry in the assembly of the RNAi enzyme complex (Reprinted from Cell, vol 115, pg 199-208, 2003). Cell 131 30 40 14567917
  13. [13]Okamura K Phillips MD Tyler DM Duan H Chou YT 2008 The regulatory activity of microRNA star species has substantial influence on microRNA and 3 ' UTR evolution. Nature Structural & Molecular Biology 15 354 363 PMC2698667 18376413
  14. [14]O'Toole AS Miller S Haines N Zink MC Serra MJ 2006 Comprehensive thermodynamic analysis of 3 ' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. Nucleic Acids Research 34 3338 3344 16820533 PMC1500867
  15. [15]Grimson A Srivastava M Fahey B Woodcroft BJ Chiang HR 2008 Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455 1193 U1115 18830242 PMC3837422
  16. [16]Hwang HW Wentzel EA Mendell JT 2007 A hexanucleotide element directs microRNA nuclear import. Science 315 97 100 17204650
  17. [17]Khvorova A Reynolds A Jayasena SD 2003 Functional siRNAs and rniRNAs exhibit strand bias. Cell 115 209 216 14567918
  18. [18]Ro S Park C Young D Sanders KM Yan W 2007 Tissue-dependent paired expression of miRNAs. Nucleic Acids Research 35 5944 5953 17726050 PMC2034466
  19. [19]Jagadeeswaran G Zheng Y Sumathipala N Jiang HB Arrese EL 2010 Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. Bmc Genomics 11 52 20089182 PMC2824724
  20. [20]Ghildiyal M Xu J Seitz H Weng ZP Zamore PD 2010 Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. Rna-a Publication of the Rna Society 16 43 56 PMC2802036 19917635
  21. [21]Jazdzewski K Liyanarachchi S Swierniak M Pachucki J Ringel MD 2009 Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proceedings of the National Academy of Sciences of the United States of America 106 1502 1505 19164563 PMC2635764
  22. [22]Wheeler BM Heimberg AM Moy VN Sperling EA Holstein TW 2009 The deep evolution of metazoan microRNAs. Evolution & Development 11 50 68 19196333
  23. [23]Liu N Okamura K Tyler DM Phillips MD Chung WJ 2008 The evolution and functional diversification of animal microRNA genes. Cell Research 18 985 996 18711447 PMC2712117
  24. [24]Kim VN Han J Siomi MC 2009 Biogenesis of small RNAs in animals. Nature Reviews Molecular Cell Biology 10 126 139 19165215
  25. [25]Guo L Lu Z 2010 Analysis of isomiR from high-throughput DNA sequencing data. in press.
  26. [26]Lagos-Quintana M Rauhut R Lendeckel W Tuschl T 2001 Identification of novel genes coding for small expressed RNAs. Science 294 853 858 11679670
  27. [27]Lau NC Lim LP Weinstein EG Bartel DP 2001 An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294 858 862 11679671
  28. [28]Lee RC Ambros V 2001 An extensive class of small RNAs in Caenorhabditis elegans. Science 294 862 864 11679672
  29. [29]Chen K Rajewsky N 2007 The evolution of gene regulation by transcription factors and microRNAs. Nature Reviews Genetics 8 93 103 17230196
  30. [30]Guo L Sun BL Sang F Wang W Lu ZH 2009 Haplotype Distribution and Evolutionary Pattern of miR-17 and miR-124 Families Based on Population Analysis. PLoS ONE 4 e7944 19956752 PMC2775919
  31. [31]Hertel J Lindemeyer M Missal K Fried C Tanzer A 2006 The expansion of the metazoan microRNA repertoire. Bmc Genomics 7 25 16480513 PMC1388199
  32. [32]Niwa R Slack FJ 2007 The evolution of animal microRNA function. Current Opinion in Genetics & Development 17 145 150 17317150
  33. [33]Sempere LF Cole CN McPeek MA Peterson KJ 2006 The phylogenetic distribution of metazoan microRNAs: Insights into evolutionary complexity and constraint. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 306B 575 588 16838302
  34. [34]Heimberg AM Sempere LF Moy VN Donoghue PCJ Peterson KJ 2008 MicroRNAs and the advent of vertebrate morphological complexity. Proceedings of the National Academy of Sciences of the United States of America 105 2946 2950 18287013 PMC2268565
  35. [35]Bompfunewerer AF Flamm C Fried C Fritzsch G Hofacker IL 2005 Evolutionary patterns of non-coding RNAs. Theory in Biosciences 123 301 369 18202870
  36. [36]Cheng LC Pastrana E Tavazoie M Doetsch F 2009 miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nature Neuroscience 12 399 408 19287386 PMC2766245
  37. [37]Nelson PT Baldwin DA Kloosterman WP Kauppinen S Plasterk RHA 2006 RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. Rna-a Publication of the Rna Society 12 187 191 PMC1370897 16373485
  38. [39]Berezikov E Guryev V van de Belt J Wienholds E Plasterk RHA 2005 Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 21 24 15652478
  39. [40]Lai EC Tomancak P Williams RW Rubin GM 2003 Computational identification of Drosophila microRNA genes. Genome Biology 4 R42 12844358 PMC193629
  40. [41]Lewis BP Shih IH Jones-Rhoades MW Bartel DP Burge CB 2003 Prediction of mammalian microRNA targets. Cell 115 787 798 14697198
  41. [42]Larkin MA Blackshields G Brown NP Chenna R McGettigan PA 2007 Clustal W and clustal X version 2.0. Bioinformatics 23 2947 2948 17846036
  42. [43]Bryant D Moulton V 2004 Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution 21 255 265 14660700
  43. [44]Huson DH Bryant D 2006 Application of phylogenetic networks in evolutionary studies. Molecular biology and evolution 23 254 16221896
  44. [45]Kuchenbauer F Morin RD Argiropoulos B Petriv OI Griffith M 2008 In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Research 18 1787 1797 18849523 PMC2577858
  45. [46]Lagos-Quintana M Rauhut R Yalcin A Meyer J Lendeckel W 2002 Identification of tissue-specific microRNAs from mouse. Current Biology 12 735 739 12007417
  46. [47]Morin RD O'Connor MD Griffith M Kuchenbauer F Delaney A 2008 Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Research 18 610 621 18285502 PMC2279248
  47. [48]Ruby JG Jan C Player C Axtell MJ Lee W 2006 Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C-elegans. Cell 127 1193 1207 17174894

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Authors
Guo, L., & Lu, Z.
Venue
PLoS ONE
Published
2010-06-30
Volume
5
Issue
6
Pages
e11387
ISSN
1932-6203
Cited by
191
References
1
Language
en

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