MicroRNA biogenesis: coordinated cropping and dicing

Key Points

  • MicroRNA (miRNA) is a single-stranded RNA of 22 nucleotides in length, which is generated by an RNase-III-type enzyme from an endogenous transcript that contains a local hairpin structure.

  • miRNA functions as a guide molecule in post-transcriptional gene silencing, by base pairing with the target mRNAs, which leads to mRNA cleavage or translational repression. By silencing various target mRNAs, miRNAs have key roles in diverse regulatory pathways, including control of development timing, haematopoietic cell differentiation, apoptosis, cell proliferation and organ development.

  • miRNA genes belong to class II genes, which are transcribed by RNA polymerase II. A majority of miRNA loci are found in intronic regions of protein-coding or non-coding transcription units, whereas the others are found in exonic regions of non-coding transcription units.

  • In animals, miRNA genes are transcribed to generate long primary transcripts (pri-miRNAs), which are first cropped by RNase-III-type enzyme Drosha to release the hairpin intermediates (pre-miRNAs) in the nucleus. Drosha forms a large (500–650 kDa) complex, known as the Microprocessor complex, together with its essential cofactor DGCR8/Pasha, which contains two dsRNA-binding domains. Pre-miRNA then gets exported to the cytoplasm by exportin-5, which is a member of the Ran-dependent nuclear transport receptor family. Following arrival in the cytoplasm, pre-miRNAs are subjected to the second processing step, which is carried out by Dicer, the cytoplasmic RNase-III-type protein.

  • In plants that lack Drosha and DGCR8, it has been suggested that miRNA processing is executed by Dicer-like protein 1 (DCL1) in the nucleus and that nuclear export is mediated by HASTY, the exportin-5 homologue.


The recent discovery of microRNAs (miRNAs) took many by surprise because of their unorthodox features and widespread functions. These tiny, 22-nucleotide, RNAs control several pathways including developmental timing, haematopoiesis, organogenesis, apoptosis, cell proliferation and possibly even tumorigenesis. Among the most pressing questions regarding this unusual class of regulatory miRNA-encoding genes is how miRNAs are produced in cells and how the genes themselves are controlled by various regulatory networks.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: The structure of five pri-miRNAs.
Figure 2: Model for microRNA biogenesis.
Figure 3: Domain organization of microRNA biogenesis factors.
Figure 4: Possible mechanisms of actions for Drosha and Dicer.
Figure 5: Generation of small hairpin RNAs.


  1. 1

    Ambros, V. et al. A uniform system for microRNA annotation. RNA 9, 277–279 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2

    Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004).

    CAS  PubMed  Google Scholar 

  3. 3

    Cullen, B. R. Transcription and processing of human microRNA precursors. Mol. Cell 16, 861–865 (2004).

    CAS  PubMed  Google Scholar 

  4. 4

    Lewis, B. P., Shih, I. H., Jones Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell 115, 787–798 (2003).

    CAS  PubMed  Google Scholar 

  5. 5

    Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).

    CAS  PubMed  Google Scholar 

  6. 6

    Bartel, D. P. & Chen, C. Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Rev. Genet. 5, 396–400 (2004).

    CAS  PubMed  Google Scholar 

  7. 7

    Kim, V. N. Small RNAs: classification, biogenesis, and function. Mol. Cells 19, 1–15 (2005).

    CAS  PubMed  Google Scholar 

  8. 8

    Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001).

    CAS  PubMed  Google Scholar 

  9. 9

    Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853–858 (2001).

    CAS  PubMed  Google Scholar 

  10. 10

    Mourelatos, Z. et al. miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Cai, X., Hagedorn, C. H. & Cullen, B. R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10, 1957–1966 (2004). This paper, together with reference 11, presents direct evidence for the pol-II-dependent transcription of miRNA genes and delineates the structure of miRNA genes.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13

    Lee, Y., Jeon, K., Lee, J. T., Kim, S. & Kim, V. N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663–4670 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Smalheiser, N. R. EST analyses predict the existence of a population of chimeric microRNA precursor–mRNA transcripts expressed in normal human and mouse tissues. Genome Biol. 4, 403 (2003).

    PubMed  PubMed Central  Google Scholar 

  15. 15

    Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L. & Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902–1910 (2004). Analyses the genomic locations of miRNA genes relative to defined transcription units.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    Aukerman, M. J. & Sakai, H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15, 2730–2741 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Tam, W. Identification and characterization of human BIC, a gene on chromosome 21 that encodes a noncoding RNA. Gene 274, 157–167 (2001).

    CAS  PubMed  Google Scholar 

  18. 18

    Bracht, J., Hunter, S., Eachus, R., Weeks, P. & Pasquinelli, A. E. Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA 10, 1586–1594 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19

    Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993). This article reports the discovery of the first miRNA.

    CAS  PubMed  Google Scholar 

  20. 20

    Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B. & Cohen, S. M. bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36 (2003).

    CAS  PubMed  Google Scholar 

  21. 21

    Lagos-Quintana, M. et al. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12, 735–739 (2002).

    CAS  PubMed  Google Scholar 

  22. 22

    Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337–350 (2003).

    CAS  PubMed  Google Scholar 

  23. 23

    Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K. & Kosik, K. S. A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9, 1274–1281 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24

    Sempere, L. F., Sokol, N. S., Dubrovsky, E. B., Berger, E. M. & Ambros, V. Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity. Dev. Biol. 259, 9–18 (2003).

    CAS  PubMed  Google Scholar 

  25. 25

    Sempere, L. F. et al. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 5, R13 (2004).

    PubMed  PubMed Central  Google Scholar 

  26. 26

    Calin, G. A. et al. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl Acad. Sci. USA 101, 11755–11760 (2004).

    CAS  PubMed  Google Scholar 

  27. 27

    Liu, C. G. et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl Acad. Sci. USA 101, 9740–9744 (2004).

    CAS  PubMed  Google Scholar 

  28. 28

    Schmittgen, T. D., Jiang, J., Liu, Q. & Yang, L. A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res. 32, e43 (2004).

    PubMed  PubMed Central  Google Scholar 

  29. 29

    Babak, T., Zhang, W., Morris, Q., Blencowe, B. J. & Hughes, T. R. Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 10, 1813–1819 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Barad, O. et al. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14, 2486–2494 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31

    Miska, E. A. et al. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5, R68 (2004).

    PubMed  PubMed Central  Google Scholar 

  32. 32

    Sun, Y. et al. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res. 32, e188 (2004).

    PubMed  PubMed Central  Google Scholar 

  33. 33

    Johnson, S. M., Lin, S. Y. & Slack, F. J. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev. Biol. 259, 364–379 (2003).

    CAS  PubMed  Google Scholar 

  34. 34

    Zeng, Y., Wagner, E. J. & Cullen, B. R. Both natural and designed micro RNAs can inhibit the eExpression of cognate mRNAs when expressed in human cells. Mol. Cell 9, 1327–1333 (2002).

    CAS  PubMed  Google Scholar 

  35. 35

    Ohler, U., Yekta, S., Lim, L. P., Bartel, D. P. & Burge, C. B. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10, 1309–1322 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 36

    Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003). This paper demonstrates the function of Drosha in primary miRNA processing.

    CAS  PubMed  Google Scholar 

  37. 37

    Filippov, V., Solovyev, V., Filippova, M. & Gill, S. S. A novel type of RNase III family proteins in eukaryotes. Gene 245, 213–221 (2000).

    CAS  PubMed  Google Scholar 

  38. 38

    Fortin, K. R., Nicholson, R. H. & Nicholson, A. W. Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location. BMC Genomics 3, 26 (2002).

    PubMed  PubMed Central  Google Scholar 

  39. 39

    Wu, H., Xu, H., Miraglia, L. J. & Crooke, S. T. Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J. Biol. Chem. 275, 36957–36965 (2000).

    CAS  PubMed  Google Scholar 

  40. 40

    Han, J. et al. The Drosha–DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027 (2004). The authors delineate the domain structure of Drosha, a class-II RNase III protein, and confirm the 'single processing centre' model.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F. & Hannon, G. J. Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235 (2004).

    CAS  PubMed  Google Scholar 

  42. 42

    Gregory, R. I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).

    CAS  PubMed  Google Scholar 

  43. 43

    Landthaler, M., Yalcin, A. & Tuschl, T. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol. 14, 2162–2167 (2004). References 40–43 report DGCR8/Pasha as the essential cofactor for Drosha.

    CAS  PubMed  Google Scholar 

  44. 44

    Zeng, Y. & Cullen, B. R. Sequence requirements for micro RNA processing and function in human cells. RNA 9, 112–123 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45

    Zeng, Y., Yi, R. & Cullen, B. R. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J. 24, 138–148 (2005).

    CAS  PubMed  Google Scholar 

  46. 46

    Kim, V. N. MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol. 14, 156–159 (2004).

    CAS  PubMed  Google Scholar 

  47. 47

    Murchison, E. P. & Hannon, G. J. miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr. Opin. Cell Biol. 16, 223–229 (2004).

    CAS  PubMed  Google Scholar 

  48. 48

    Nakielny, S. & Dreyfuss, G. Transport of proteins and RNAs in and out of the nucleus. Cell 99, 677–690 (1999).

    CAS  PubMed  Google Scholar 

  49. 49

    Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004).

    CAS  PubMed  Google Scholar 

  50. 50

    Yi, R., Qin, Y., Macara, I. G. & Cullen, B. R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17, 3011–3016 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51

    Bohnsack, M. T., Czaplinski, K. & Gorlich, D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10, 185–191 (2004). Together with references 49 and 50, this paper shows that exportin-5 mediates the nuclear export of pre-miRNAs.

    CAS  PubMed  PubMed Central  Google Scholar 

  52. 52

    Bohnsack, M. T. et al. Exp5 exports eEF1A via tRNA from nuclei and synergizes with other transport pathways to confine translation to the cytoplasm. EMBO J. 21, 6205–6215 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53

    Calado, A., Treichel, N., Muller, E. C., Otto, A. & Kutay, U. Exportin-5-mediated nuclear export of eukaryotic elongation factor 1A and tRNA. EMBO J. 21, 6216–6224 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54

    Lim, L. P. et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 2, 991–1008 (2003).

    Google Scholar 

  55. 55

    Gwizdek, C. et al. Exportin-5 mediates nuclear export of minihelix-containing RNAs. J. Biol. Chem. 278, 5505–5508 (2003).

    CAS  PubMed  Google Scholar 

  56. 56

    Basyuk, E., Suavet, F., Doglio, A., Bordonne, R. & Bertrand, E. Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res. 31, 6593–6597 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57

    Zeng, Y. & Cullen, B. R. Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res. 32, 4776–4785 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001).

    CAS  PubMed  Google Scholar 

  59. 59

    Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001).

    CAS  PubMed  Google Scholar 

  60. 60

    Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001).

    CAS  PubMed  Google Scholar 

  61. 61

    Ketting, R. F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654–2659 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62

    Knight, S. W. & Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269–2271 (2001). References 58–62 reveal the key role of Dicer in small-RNA pathways.

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 63

    Hammond, S. M., Bernstein, E., Beach, D. & Hannon, G. J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293–296 (2000).

    CAS  PubMed  Google Scholar 

  64. 64

    Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65

    Ma, J. B., Ye, K. & Patel, D. J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318–322 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66

    Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain. Nature Struct. Mol. Biol. 11, 576–577 (2004).

    CAS  Google Scholar 

  67. 67

    Song, J. J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Struct. Biol. 10, 1026–1032 (2003).

    CAS  PubMed  Google Scholar 

  68. 68

    Yan, K. S. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468–474 (2003).

    PubMed  PubMed Central  Google Scholar 

  69. 69

    Tabara, H., Yigit, E., Siomi, H. & Mello, C. C. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell 109, 861–871 (2002).

    CAS  PubMed  Google Scholar 

  70. 70

    Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921–1925 (2003).

    CAS  PubMed  Google Scholar 

  71. 71

    Ishizuka, A., Siomi, M. C. & Siomi, H. A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins. Genes Dev. 16, 2497–2508 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. 72

    Caudy, A. A., Myers, M., Hannon, G. J. & Hammond, S. M. Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev. 16, 2491–2496 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. 73

    Jin, P. et al. Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nature Neurosci. 7, 113–117 (2004).

    CAS  PubMed  Google Scholar 

  74. 74

    Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150 (2001).

    CAS  PubMed  Google Scholar 

  75. 75

    Carmell, M. A., Xuan, Z., Zhang, M. Q. & Hannon, G. J. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16, 2733–2742 (2002).

    CAS  PubMed  Google Scholar 

  76. 76

    Zhang, H., Kolb, F. A., Brondani, V., Billy, E. & Filipowicz, W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875–5885 (2002). This paper presents a new model for the mechanism of action for RNase III proteins.

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 77

    Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. & Filipowicz, W. Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57–68 (2004).

    CAS  PubMed  Google Scholar 

  78. 78

    Song, J. J., Smith, S. K., Hannon, G. J. & Joshua-Tor, L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305, 1434–1437 (2004).

    CAS  PubMed  Google Scholar 

  79. 79

    Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437–1441 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. 80

    Meister, G. et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185–197 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. 81

    Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).

    CAS  PubMed  Google Scholar 

  82. 82

    Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003).

    CAS  PubMed  Google Scholar 

  83. 83

    Tomari, Y., Matranga, C., Haley, B., Martinez, N. & Zamore, P. D. A protein sensor for siRNA asymmetry. Science 306, 1377–1380 (2004).

    CAS  PubMed  Google Scholar 

  84. 84

    Park, W. et al. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12, 1484–1495 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 85

    Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B. & Bartel, D. P. MicroRNAs in plants. Genes Dev. 16, 1616–1626 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. 86

    Papp, I. et al. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol. 132, 1382–1390 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. 87

    Kurihara, Y. & Watanabe, Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl Acad. Sci. USA 101, 12753–12758 (2004).

    CAS  PubMed  Google Scholar 

  88. 88

    Xie, Z. et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104 (2004).

    PubMed  PubMed Central  Google Scholar 

  89. 89

    Bollman, K. M. et al. HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 130, 1493–1504 (2003).

    CAS  PubMed  Google Scholar 

  90. 90

    Telfer, A. & Poethig, R. S. HASTY: a gene that regulates the timing of shoot maturation in Arabidopsis thaliana. Development 125, 1889–1898 (1998).

    CAS  PubMed  Google Scholar 

  91. 91

    Park, M. Y. et al. Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl Acad. Sci. USA 102, 3691–3696 (2005).

    CAS  PubMed  Google Scholar 

  92. 92

    Vazquez, F., Gasciolli, V., Crete, P. & Vaucheret, H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 14, 346–351 (2004).

    CAS  PubMed  Google Scholar 

  93. 93

    Han, M. H., Goud, S., Song, L. & Fedoroff, N. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl Acad. Sci. USA 101, 1093–1098 (2004).

    CAS  PubMed  Google Scholar 

  94. 94

    Boutet, S. et al. Arabidopsis HEN1. A genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol. 13, 843–848 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. 95

    Yu, B. et al. Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932–935 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. 96

    Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807–818 (2003).

    CAS  PubMed  Google Scholar 

  97. 97

    Hannon, G. J. & Rossi, J. J. Unlocking the potential of the human genome with RNA interference. Nature 431, 371–378 (2004).

    CAS  PubMed  Google Scholar 

  98. 98

    Yi, R., Doehle, B. P., Qin, Y., Macara, I. G. & Cullen, B. R. Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA 11, 220–226 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99

    Zeng, Y., Cai, X. & Cullen, B. R. Use of RNA polymerase II to transcribe artificial microRNAs. Methods Enzymol. 392, 371–380 (2005).

    CAS  PubMed  Google Scholar 

  100. 100

    Ambros, V. The functions of animal microRNAs. Nature 431, 350–355 (2004).

    CAS  PubMed  Google Scholar 

  101. 101

    Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855–862 (1993).

    CAS  PubMed  Google Scholar 

  102. 102

    Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906 (2000).

    CAS  PubMed  Google Scholar 

  103. 103

    Chang, S., Johnston, R. J., Jr., Frokjaer-Jensen, C., Lockery, S. & Hobert, O. MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430, 785–789 (2004).

    CAS  PubMed  Google Scholar 

  104. 104

    Johnston, R. J. & Hobert, O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845–849 (2003).

    CAS  PubMed  Google Scholar 

  105. 105

    Chen, C. Z., Li, L., Lodish, H. F. & Bartel, D. P. MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86 (2004).

    CAS  PubMed  Google Scholar 

  106. 106

    Yekta, S., Shih, I. H. & Bartel, D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594–596 (2004).

    CAS  PubMed  Google Scholar 

  107. 107

    Xu, P., Vernooy, S. Y., Guo, M. & Hay, B. A. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13, 790–795 (2003).

    CAS  PubMed  Google Scholar 

  108. 108

    Esau, C. et al. MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem. 279, 52361–52365 (2004).

    CAS  PubMed  Google Scholar 

  109. 109

    Vazquez, F. et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16, 69–79 (2004).

    CAS  PubMed  Google Scholar 

  110. 110

    Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H. L. & Poethig, R. S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 18, 2368–2379 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. 111

    Hamilton, A., Voinnet, O., Chappell, L. & Baulcombe, D. Two classes of short interfering RNA in RNA silencing. EMBO J. 21, 4671–4679 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. 112

    Llave, C., Kasschau, K. D., Rector, M. A. & Carrington, J. C. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605–1619 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. 113

    Mette, M. F., van der Winden, J., Matzke, M. & Matzke, A. J. Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiol. 130, 6–9 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. 114

    Djikeng, A., Shi, H., Tschudi, C. & Ullu, E. RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24–26-nucleotide RNAs. RNA 7, 1522–1530 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. 115

    Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001).

    CAS  PubMed  Google Scholar 

  116. 116

    Aravin, A. A. et al. Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol. Cell. Biol. 24, 6742–6750 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. 117

    Pal-Bhadra, M., Bhadra, U. & Birchler, J. A. RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell 9, 315–327 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. 118

    Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002).

    CAS  PubMed  Google Scholar 

  119. 119

    Reinhart, B. J. & Bartel, D. P. Small RNAs correspond to centromere heterochromatic repeats. Science 297, 1831 (2002).

    CAS  Google Scholar 

  120. 120

    Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002).

    CAS  PubMed  Google Scholar 

  121. 121

    Zilberman, D., Cao, X. & Jacobsen, S. E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299, 716–719 (2003).

    CAS  PubMed  Google Scholar 

  122. 122

    Mochizuki, K., Fine, N. A., Fujisawa, T. & Gorovsky, M. A. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell 110, 689–699 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. 123

    Liu, Y., Mochizuki, K. & Gorovsky, M. A. Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena. Proc. Natl Acad. Sci. USA 101, 1679–1684 (2004).

    CAS  PubMed  Google Scholar 

  124. 124

    Taverna, S. D., Coyne, R. S. & Allis, C. D. Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena. Cell 110, 701–711 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  125. 125

    Kuwabara, T., Hsieh, J., Nakashima, K., Taira, K. & Gage, F. H. A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116, 779–793 (2004).

    CAS  PubMed  Google Scholar 

  126. 126

    Calin, G. A. et al. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl Acad. Sci. USA 99, 15524–15529 (2002).

    CAS  PubMed  Google Scholar 

  127. 127

    Blaszczyk, J. et al. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure (Camb.) 9, 1225–1236 (2001).

    CAS  Google Scholar 

  128. 128

    Poy, M. N. et al. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226–230 (2004).

    CAS  PubMed  Google Scholar 

Download references


I am grateful to members of my laboratory, especially to Young Kook Kim for the bioinformatics analysis of the miRNA gene structure. This work was supported by a Molecular and Cellular BioDiscovery Research Program grant from the Ministry of Science and Technology and a Research Fellowship from the Ministry of Education and Human Resources Development of Korea.

Author information



Ethics declarations

Competing interests

The author declares no competing financial interests.

Related links

Related links


Entrez Gene










The miRNA Registry














V. Narry Kim's laboratory

Noncoding RNAs Database

RNA & DNA Folding Applications

The miRNA Registry



(siRNA; also known as short interfering RNA). A small (21–24 nucleotide), non-coding RNA that is generated from long double-stranded RNA. siRNAs function as guide molecules in small-RNA-mediated gene silencing.


A transcript that includes regions representing multiple, non-overlapping gene products.


A structure, which consists of m7GpppN (where m7G represents 7-methylguanylate, p represents a phosphate group and N represents any base), that is located at the 5′ end of eukaryotic mRNAs.


A homopolymeric stretch of usually 25–200 adenine nucleotides that is present at the 3′ end of most eukaryotic mRNAs.


(snoRNAs). A small RNA molecule that functions in ribosome biogenesis in the nucleolus by guiding the assembly of macromolecular complexes on the target RNA to allow site-specific modifications or processing reactions to occur.


Intermolecular splicing that occurs in trypanosomes and worms where a short sequence (SL RNA) is linked to the 5′ end of many pre-mRNAs.


A protein domain that binds to proline-rich regions.


An evolutionarily conserved domain in a family of enzymes that use ATP hydrolysis to unwind RNA duplexes. The domain is named after the DEAD (Asp-Glu-Ala-Asp) motif.


A conserved RNA-binding domain found in members of the Dicer and Argonaute protein families, and that preferentially interacts with the 3′ end of RNA.


(also known as PPD proteins). A family of proteins that are characterized by the presence of two homology domains, PAZ and PIWI. These proteins are essential for diverse small-RNA pathways.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kim, V. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6, 376–385 (2005). https://doi.org/10.1038/nrm1644

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing