MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. miRNAs are transcribed as precursor molecules, which are subsequently cleaved by the endoribonucleases Drosha and Dicer. Mature miRNAs are bound by a member of the Argonaute (AGO) protein family to form the RNA-induced silencing complex (RISC) in a process termed RISC loading. Advances in structural analyses of Drosha and Dicer complexes enabled elucidation of the mechanisms that drive these molecular machines. Transcription of miRNAs, their processing by Drosha and Dicer and RISC loading are key steps in miRNA biogenesis, and various additional factors facilitate, support or inhibit these processes. Recent work has revealed that regulatory factors not only coordinate individual miRNA processing steps but also connect miRNA biogenesis with other cellular processes. Protein phosphorylation, for example, links miRNA biogenesis to various signalling pathways, and such modifications are often associated with disease. Furthermore, not all miRNAs follow canonical processing routes, and many non-canonical miRNA biogenesis pathways have recently been characterized.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $22.08 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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).
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). References 1 and 2 show that miRNAs exist in C. elegans and have the potential to regulate complementary target genes.
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).
Lee, R. C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001).
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853–858 (2001). This study reports the identification of mammalian miRNAs.
Baumann, V. & Winkler, J. miRNA-based therapies: strategies and delivery platforms for oligonucleotide and non-oligonucleotide agents. Future Med. Chem. 6, 1967–1984 (2014).
Carthew, R. W. & Sontheimer, E. J. Origins and mechanisms of mi-RNAs and siRNAs. Cell 136, 642–655 (2009).
Ha, M. & Kim, V. N. Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol. 15, 509–524 (2014).
Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009).
Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060 (2004).
Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003). This study characterizes the RNase III enzyme Drosha as the enzyme responsible for converting pri-miRNAs into pre-miRNAs.
Gregory, R. I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).
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).
Han, J. et al. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027 (2004).
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).
Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004).
Bohnsack, M. T., Czaplinski, K. & Gorlich, D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-mi-RNAs. RNA 10, 185–191 (2004).
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). References 16–18 identify Exp5 as the export receptor that is required for exporting pre-miRNAs into the cytoplasm.
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).
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). References 19 and 20 identify Dicer as the RNase III enzyme that further processes pre-miRNAs into mature miRNAs.
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).
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).
Kobayashi, H. & Tomari, Y. RISC assembly: coordination between small RNAs and Argonaute proteins. Biochim. Biophys. Acta 1859, 71–81 (2016).
Kim, Y. K., Kim, B. & Kim, V. N. Re-evaluation of the roles of DROSHA, export in 5, and DICER in microRNA biogenesis. Proc. Natl Acad. Sci. USA 113, E1881–1889 (2016).
Conrad, T., Marsico, A., Gehre, M. & Orom, U. A. Microprocessor activity controls differential miRNA biogenesis In Vivo. Cell Rep. 9, 542–554 (2014).
Roden, C. et al. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Genome Res. 27, 374–384 (2017).
Auyeung, V. C., Ulitsky, I., McGeary, S. E. & Bartel, D. P. Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152, 844–858 (2013).
Fang, W. & Bartel, D. P. The menu of features that define primary microRNAs and enable de novo design of microRNA genes. Mol. Cell 60, 131–145 (2015). References 27 and 28 identify sequence features of pri-miRNAs that are important for their efficient processing.
Michlewski, G., Guil, S., Semple, C. A. & Caceres, J. F. Posttranscriptional regulation of mi-RNAs harboring conserved terminal loops. Mol. Cell 32, 383–393 (2008).
Concepcion, C. P., Bonetti, C. & Ventura, A. The microRNA-17-92 family of microRNA clusters in development and disease. Cancer J. 18, 262–267 (2012).
Chaulk, S. G. et al. Role of pri-miRNA tertiary structure in miR-17~92 miRNA biogenesis. RNA Biol. 8, 1105–1114 (2011).
Chakraborty, S. & Krishnan, Y. A structural map of oncomiR-1 at single-nucleotide resolution. Nucleic Acids Res. 45, 9694–9705 (2017).
Du, P., Wang, L., Sliz, P. & Gregory, R. I. A. Biogenesis step upstream of microprocessor controls miR-17 approximately 92 expression. Cell 162, 885–899 (2015).
Contrant, M. et al. Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs. Nucleic Acids Res. 42, 7981–7996 (2014).
Rouleau, S. G., Garant, J. M., Bolduc, F., Bisaillon, M. & Perreault, J. P. G-Quadruplexes influence pri-microRNA processing. RNA Biol 15, 198–206 (2018).
Fernandez, N. et al. Genetic variation and RNA structure regulate microRNA biogenesis. Nat. Commun. 8, 15114 (2017).
Han, J. et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125, 887–901 (2006).
Sohn, S. Y. et al. Crystal structure of human DGCR8 core. Nat. Struct. Mol. Biol. 14, 847–853 (2007).
Faller, M., Matsunaga, M., Yin, S., Loo, J. A. & Guo, F. Heme is involved in microRNA processing. Nat. Struct. Mol. Biol. 14, 23–29 (2007).
Senturia, R. et al. Structure of the dimerization domain of DiGeorge critical region 8. Protein Sci. 19, 1354–1365 (2010).
Quick-Cleveland, J. et al. The DGCR8 RNA-binding heme domain recognizes primary microRNAs by clamping the hairpin. Cell Rep. 7, 1994–2005 (2014).
Weitz, S. H., Gong, M., Barr, I., Weiss, S. & Guo, F. Processing of microRNA primary transcripts requires heme in mammalian cells. Proc. Natl Acad. Sci. USA 111, 1861–1866 (2014).
Partin, A. C. et al. Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs. Nat. Commun. 8, 1737 (2017).
Nguyen, T. A. et al. functional anatomy of the human microprocessor. Cell 161, 1374–1387 (2015).
Herbert, K. M. et al. A heterotrimer model of the complete microprocessor complex revealed by single-molecule subunit counting. RNA 22, 175–183 (2016).
Kwon, S. C. et al. Structure of human DROSHA. Cell 164, 81–90 (2016). This paper clarifies the mechanism of action of Drosha by solving the crystal structure of a large Drosha fragment.
Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. & Filipowicz, W. Single processing center models for human Dicer & bacterial RNase III. Cell 118, 57–68 (2004).
Macrae, I. J. et al. Structural basis for double-stranded RNA processing by Dicer. Science 311, 195–198 (2006). This paper presents the crystallization of Dicer from G. intestinalis , which provides molecular details of Dicer function.
Liu, Z. et al. Cryo-EM structure of human dicer and its complexes with a pre-miRNA substrate. Cell 173, 1191–1203 (2018).
Taylor, D. W. et al. Substrate-specific structural rearrangements of human Dicer. Nat. Struct. Mol. Biol. 20, 662–670 (2013).
Lau, P. W. et al. The molecular architecture of human Dicer. Nat. Struct. Mol. Biol. 19, 436–440 (2012).
Tian, Y. et al. A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer. Mol. Cell 53, 606–616 (2014).
Haase, A. D. et al. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep. 6, 961–967 (2005).
Chendrimada, T. P. et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436, 740–744 (2005).
Wilson, R. C. et al. Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis. Mol. Cell 57, 397–407 (2015).
Jakob, L. et al. Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA 22, 383–396 (2016).
Ota, H. et al. ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing. Cell 153, 575–589 (2013).
Meister, G. Argonaute proteins: functional insights and emerging roles. Nat. Rev. Genet. 14, 447–459 (2013).
Ipsaro, J. J. & Joshua-Tor, L. From guide to target: molecular insights into eukaryotic RNA-interference machinery. Nat. Struct. Mol. Biol. 22, 20–28 (2015).
Gregory, R. I., Chendrimada, T. P., Cooch, N. & Shiekhattar, R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123, 631–640 (2005).
Meister, G. et al. Identification of novel argonaute-associated proteins. Curr. Biol. 15, 2149–2155 (2005).
Wang, H. W. et al. Structural insights into RNA processing by the human RISC-loading complex. Nat. Struct. Mol. Biol. 16, 1148–1153 (2009).
MacRae, I. J., Ma, E., Zhou, M., Robinson, C. V. & Doudna, J. A. In vitro reconstitution of the human RISC-loading complex. Proc. Natl Acad. Sci. USA 105, 512–517 (2008).
Kwak, P. B. & Tomari, Y. The N domain of Argonaute drives duplex unwinding during RISC assembly. Nat. Struct. Mol. Biol. 19, 145–151 (2012).
Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).
Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and mi-RNAs exhibit strand bias. Cell 115, 209–216 (2003).
Park, J. H. & Shin, C. Slicer-independent mechanism drives small-RNA strand separation during human RISC assembly. Nucleic Acids Res. 43, 9418–9433 (2015).
Suzuki, H. I. et al. Small-RNA asymmetry is directly driven by mammalian Argonautes. Nat. Struct. Mol. Biol. 22, 512–521 (2015).
Matranga, C., Tomari, Y., Shin, C., Bartel, D. P. & Zamore, P. D. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607–620 (2005).
Rand, T. A., Petersen, S., Du, F. & Wang, X. Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123, 621–629 (2005).
Leuschner, P. J., Ameres, S. L., Kueng, S. & Martinez, J. Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep. 7, 314–320 (2006).
Sheu-Gruttadauria, J. & MacRae, I. J. Structural foundations of RNA silencing by Argonaute. J. Mol. Biol. 429, 2619–2639 (2017).
Nakanishi, K. Anatomy of RISC: how do small RNAs and chaperones activate Argonaute proteins? Wiley Interdiscip Rev. RNA 7, 637–660 (2016).
Iki, T. et al. In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90. Mol. Cell 39, 282–291 (2010).
Iwasaki, S. et al. Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes. Mol. Cell 39, 292–299 (2010).
Johnston, M., Geoffroy, M. C., Sobala, A., Hay, R. & Hutvagner, G. HSP90 protein stabilizes unloaded argonaute complexes and microscopic P-bodies in human cells. Mol. Biol. Cell 21, 1462–1469 (2010).
Miyoshi, T., Takeuchi, A., Siomi, H. & Siomi, M. C. A direct role for Hsp90 in pre-RISC formation in Drosophila. Nat. Struct. Mol. Biol. 17, 1024–1026 (2010).
Kawamata, T., Yoda, M. & Tomari, Y. Multilayer checkpoints for microRNA authenticity during RISC assembly. EMBO Rep. 12, 944–949 (2011).
Koh, H. R., Ghanbariniaki, A. & Myong, S. RNA stem structure governs coupling of dicing and gene silencing in RNA interference. Proc. Natl Acad. Sci. USA 114, E10349–E10358 (2017).
Yoda, M. et al. ATP-dependent human RISC assembly pathways. Nat. Struct. Mol. Biol. 17, 17–23 (2010).
Herbert, K. M., Pimienta, G., DeGregorio, S. J., Alexandrov, A. & Steitz, J. A. Phosphorylation of DGCR8 increases its intracellular stability and induces a progrowth miRNA profile. Cell Rep. 5, 1070–1081 (2013).
Paroo, Z., Ye, X., Chen, S. & Liu, Q. Phosphorylation of the human microRNA-generating complex mediates MAPK/Erk signaling. Cell 139, 112–122 (2009).
Warner, M. J. et al. S6K2-mediated regulation of TRBP as a determinant of miRNA expression in human primary lymphatic endothelial cells. Nucleic Acids Res. 44, 9942–9955 (2016).
Drake, M. et al. A requirement for ERK-dependent Dicer phosphorylation in coordinating oocyte-to-embryo transition in C. elegans. Dev. Cell 31, 614–628 (2014).
Coulthard, L. R., White, D. E., Jones, D. L., McDermott, M. F. & Burchill, S. A. p38(MAPK): stress responses from molecular mechanisms to therapeutics. Trends Mol. Med. 15, 369–379 (2009).
Yang, Q. et al. Stress induces p38 MAPK-mediated phosphorylation and inhibition of Drosha-dependent cell survival. Mol. Cell 57, 721–734 (2015).
Hong, S. et al. Signaling by p38 MAPK stimulates nuclear localization of the microprocessor component p68 for processing of selected primary microRNAs. Sci. Signal 6, ra16 (2013).
Tu, C. C. et al. The kinase ABL phosphorylates the microprocessor subunit DGCR8 to stimulate primary microRNA processing in response to DNA damage. Sci. Signal 8, ra64 (2015).
Tang, X., Zhang, Y., Tucker, L. & Ramratnam, B. Phosphorylation of the RNase III enzyme Drosha at Serine300 or Serine302 is required for its nuclear localization. Nucleic Acids Res. 38, 6610–6619 (2010).
Fletcher, C. E., Godfrey, J. D., Shibakawa, A., Bushell, M. & Bevan, C. L. A novel role for GSK3beta as a modulator of Drosha microprocessor activity and MicroRNA biogenesis. Nucleic Acids Res. 45, 2809–2828 (2016).
Shen, J. et al. EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2. Nature 497, 383–387 (2013).
Yang, M. et al. Dephosphorylation of tyrosine 393 in argonaute 2 by protein tyrosine phosphatase 1B regulates gene silencing in oncogenic RAS-induced senescence. Mol. Cell 55, 782–790 (2014).
Saxton, R. A. & Sabatini, D. M. mTOR signaling in growth, metabolism, and disease. Cell 168, 960–976 (2017).
Ye, P. et al. An mTORC1-Mdm2-Drosha axis for miRNA biogenesis in response to glucose- and amino acid-deprivation. Mol. Cell 57, 708–720 (2015).
Di Leva, G., Garofalo, M. & Croce, C. M. MicroRNAs in cancer. Annu. Rev. Pathol. 9, 287–314 (2014).
Zhu, C. et al. SUMOylation at K707 of DGCR8 controls direct function of primary microRNA. Nucleic Acids Res. 43, 7945–7960 (2015).
Chen, C. et al. SUMOylation of TARBP2 regulates miRNA/siRNA efficiency. Nat. Commun. 6, 8899 (2015).
Mayr, F., Schutz, A., Doge, N. & Heinemann, U. The Lin28 cold-shock domain remodels pre-let-7 microRNA. Nucleic Acids Res. 40, 7492–7506 (2012).
Roush, S. & Slack, F. J. The let-7 family of microRNAs. Trends Cell Biol. 18, 505–516 (2008).
Triboulet, R., Pirouz, M. & Gregory, R. I. A. Single let-7 MicroRNA bypasses LIN28-mediated repression. Cell Rep. 13, 260–266 (2015).
Ustianenko, D. et al. LIN28 selectively modulates a subset of let-7 microRNAs. Mol. Cell 71, 271–283 (2018).
Newman, M. A., Thomson, J. M. & Hammond, S. M. Lin-28 interaction with the let-7 precursor loop mediates regulated microRNA processing. Rna 14, 1539–1549 (2008).
Heo, I. et al. Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol. Cell 32, 276–284 (2008).
Heo, I. et al. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 138, 696–708 (2009).
Viswanathan, S. R., Daley, G. Q. & Gregory, R. I. Selective blockade of microRNA processing by Lin28. Science 320, 97–100 (2008).
Rybak, A. et al. A feedback loop comprising Lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nat. Cell Biol. 10, 987–993 (2008).
Thornton, J. E. et al. Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4). Nucleic Acids Res. 42, 11777–11791 (2014). References 103–107 show that LIN28 regulates pre-let-7 processing by recruiting TUTases to let-7 miRNA precursors in stem cells.
Chang, H. M., Triboulet, R., Thornton, J. E. & Gregory, R. I. A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway. Nature 497, 244–248 (2013).
Faehnle, C. R., Walleshauser, J. & Joshua-Tor, L. Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway. Nature 514, 252–256 (2014).
Ustianenko, D. et al. Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 mi-RNAs. RNA 19, 1632–1638 (2013).
Heo, I. et al. Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell 151, 521–532 (2012).
Kim, B. et al. TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms. EMBO J. 34, 1801–1815 (2015).
Wang, L. et al. LIN28 zinc knuckle domain is required and sufficient to induce let-7 oligouridylation. Cell Rep. 18, 2664–2675 (2017).
Faehnle, C. R., Walleshauser, J. & Joshua-Tor, L. Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis. Nat. Struct. Mol. Biol. 24, 658–665 (2017).
Balzeau, J., Menezes, M. R., Cao, S. & Hagan, J. P. The LIN28/let-7 pathway in cancer. Front. Genet. 8, 31 (2017).
Piskounova, E. et al. Lin28A and Lin28B Inhibit let-7 microRNA biogenesis by distinct mechanisms. Cell 147, 1066–1079 (2011).
Treiber, T., Treiber, N. & Meister, G. Regulation of microRNA biogenesis and function. Thromb. Haemost. 107, 605–610 (2012).
Guil, S. & Caceres, J. F. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat. Struct. Mol. Biol. 14, 591–596 (2007).
Michlewski, G. & Caceres, J. F. Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nat. Struct. Mol. Biol. 17, 1011–1018 (2010).
Trabucchi, M. et al. The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature 459, 1010–1014 (2009).
Kim, K. K., Yang, Y., Zhu, J., Adelstein, R. S. & Kawamoto, S. Rbfox3 controls the biogenesis of a subset of microRNAs. Nat. Struct. Mol. Biol. 21, 901–910 (2014).
Wu, S. L. et al. Genome-wide analysis of YB-1-RNA interactions reveals a novel role of YB-1 in miRNA processing in glioblastoma multiforme. Nucleic Acids Res. 43, 8516–8528 (2015).
Kawahara, Y. & Mieda-Sato, A. TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes. Proc. Natl Acad. Sci. USA 109, 3347–3352 (2012).
Choudhury, N. R. et al. Tissue-specific control of brain-enriched miR-7 biogenesis. Genes Dev. 27, 24–38 (2013).
Treiber, T. et al. A compendium of RNA-binding proteins that regulate microRNA biogenesis. Mol. Cell 66, 270–284 (2017).
Nussbacher, J. K. & Yeo, G. W. Systematic discovery of RNA binding proteins that regulate microRNA levels. Mol. Cell 69, 1005–1016 (2018). References 125 and 126 report large-scale analyses of RBPs that post-transcriptionally regulate miRNA biogenesis.
Morlando, M. et al. Primary microRNA transcripts are processed co-transcriptionally. Nat. Struct. Mol. Biol. 15, 902–909 (2008).
Yin, S., Yu, Y. & Reed, R. Primary microRNA processing is functionally coupled to RNAP II transcription in vitro. Sci. Rep. 5, 11992 (2015).
Ballarino, M. et al. Coupled RNA processing and transcription of intergenic primary microRNAs. Mol. Cell. Biol. 29, 5632–5638 (2009).
Liu, H. et al. HP1BP3, a chromatin retention factor for co-transcriptional microRNA processing. Mol. Cell 63, 420–432 (2016).
Church, V. A. et al. Microprocessor recruitment to elongating RNA Polymerase II is required for differential expression of microRNAs. Cell Rep. 20, 3123–3134 (2017).
King, I. N. et al. The RNA-binding protein TDP-43 selectively disrupts microRNA-1/206 incorporation into the RNA-induced silencing complex. J. Biol. Chem. 289, 14263–14271 (2014).
Yoon, J. H. et al. AUF1 promotes let-7b loading on Argonaute 2. Genes Dev. 29, 1599–1604 (2015).
Wang, W. et al. An importin beta protein negatively regulates microRNA activity in Arabidopsis. Plant Cell 23, 3565–3576 (2011).
Cui, Y., Fang, X. & Qi, Y. TRANSPORTIN1 promotes the association of microRNA with ARGONAUTE1 in Arabidopsis. Plant Cell 28, 2576–2585 (2016).
Krol, J. et al. A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture. Nat. Commun. 6, 7305 (2015).
Ruby, J. G., Jan, C. H. & Bartel, D. P. Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83–86 (2007).
Okamura, K., Hagen, J. W., Duan, H., Tyler, D. M. & Lai, E. C. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130, 89–100 (2007). References 137 and 138 identify the mirtron pathway in flies and mammals.
Berezikov, E., Chung, W. J., Willis, J., Cuppen, E. & Lai, E. C. Mammalian mirtron genes. Mol. Cell 28, 328–336 (2007).
Meng, Y. & Shao, C. Large-scale identification of mirtrons in Arabidopsis and rice. PLOS One 7, e31163 (2012).
Flynt, A. S., Greimann, J. C., Chung, W. J., Lima, C. D. & Lai, E. C. MicroRNA biogenesis via splicing and exosome-mediated trimming in Drosophila. Mol. Cell 38, 900–907 (2010).
Valen, E. et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat. Struct. Mol. Biol. 18, 1075–1082 (2011).
Wen, J., Ladewig, E., Shenker, S., Mohammed, J. & Lai, E. C. Analysis of nearly one thousand mammalian mirtrons reveals novel features of dicer substrates. PLOS Comput. Biol. 11, e1004441 (2015).
Reimao-Pinto, M. M. et al. Uridylation of RNA hairpins by tailor confines the emergence of microRNAs in Drosophila. Mol. Cell 59, 203–216 (2015).
Bortolamiol-Becet, D. et al. Selective suppression of the splicing-mediated microRNA pathway by the terminal uridyltransferase tailor. Mol. Cell 59, 217–228 (2015).
Babiarz, J. E. et al. A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. RNA 17, 1489–1501 (2011).
Babiarz, J. E., Ruby, J. G., Wang, Y., Bartel, D. P. & Blelloch, R. Mouse ES cells express endogenous shRNAs, siRNAs, and other microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 22, 2773–2785 (2008).
Saraiya, A. A. & Wang, C. C. snoRNA, a novel precursor of microRNA in Giardia lamblia. PLOS Pathog. 4, e1000224 (2008).
Ender, C. et al. A human snoRNA with microRNA-like functions. Mol. Cell 32, 519–528 (2008).
Scott, M. S., Avolio, F., Ono, M., Lamond, A. I. & Barton, G. J. Human miRNA precursors with box H/ACA snoRNA features. PLOS Comput. Biol. 5, e1000507 (2009).
Taft, R. J. et al. Small RNAs derived from snoRNAs. RNA 15, 1233–1240 (2009).
Cole, C. et al. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15, 2147–2160 (2009).
Haussecker, D. et al. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16, 673–695 (2010).
Kumar, P., Kuscu, C. & Dutta, A. Biogenesis and function of transfer RNA-related fragments (tRFs). Trends Biochem. Sci. 41, 679–689 (2016).
Hasler, D. & Meister, G. From tRNA to miRNA: RNA-folding contributes to correct entry into noncoding RNA pathways. FEBS Lett. 590, 2354–2363 (2016).
Hasler, D. et al. The lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway. Mol. Cell 63, 110–124 (2016).
Xie, M. et al. Mammalian 5ʹ-capped microRNA precursors that generate a single microRNA. Cell 155, 1568–1580 (2013).
Martinez, I. et al. An exportin-1-dependent microRNA biogenesis pathway during human cell quiescence. Proc. Natl Acad. Sci. USA 114, E4961–E4970 (2017).
Link, S., Grund, S. E. & Diederichs, S. Alternative splicing affects the subcellular localization of Drosha. Nucleic Acids Res. 44, 5330–5343 (2016).
Cifuentes, D. et al. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 328, 1694–1698 (2010).
Cheloufi, S., Dos Santos, C. O., Chong, M. M. & Hannon, G. J. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 465, 584–589 (2010). References 160 and 161 show that miR-451 is processed by Ago2 rather than by Dicer.
Yoda, M. et al. Poly(A)-specific ribonuclease mediates 3ʹ-end trimming of Argonaute2-cleaved precursor microRNAs. Cell Rep. 5, 715–726 (2013).
Rasmussen, K. D. et al. The miR-144/451 locus is required for erythroid homeostasis. J. Exp. Med. 207, 1351–1358 (2010).
Yu, D. et al. miR-451 protects against erythroid oxidant stress by repressing 14-3-3zeta. Genes Dev. 24, 1620–1633 (2010).
Patrick, D. M. et al. Defective erythroid differentiation in miR-451 mutant mice mediated by 14-3-3zeta. Genes Dev. 24, 1614–1619 (2010).
Jee, D. et al. Dual strategies for Argonaute2-mediated biogenesis of erythroid mi-RNAs underlie conserved requirements for slicing in mammals. Mol. Cell 69, 265–278 (2018).
Diederichs, S. & Haber, D. A. Dual role for argonautes in microRNA processing and posttranscrcptional regulation of microRNA expression. Cell 131, 1097–1108 (2007).
Gadd, S. et al. A children’s oncology group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nat. Genet. 49, 1487–1494 (2017).
Walz, A. L. et al. Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors. Cancer Cell 27, 286–297 (2015).
Wegert, J. et al. Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors. Cancer Cell 27, 298–311 (2015).
Torrezan, G. T. et al. Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour. Nat. Commun. 5, 4039 (2014).
Rakheja, D. et al. Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours. Nat. Commun. 2, 4802 (2014).
Hata, A. & Kashima, R. Dysregulation of microRNA biogenesis machinery in cancer. Crit. Rev. Biochem. Mol. Biol. 51, 121–134 (2016).
Foulkes, W. D., Priest, J. R. & Duchaine, T. F. DICER1: mutations, microRNAs and mechanisms. Nat. Rev. Cancer 14, 662–672 (2014).
Hill, D. A. et al. DICER1 mutations in familial pleuropulmonary blastoma. Science 325, 965 (2009).
Durieux, E. et al. The co-occurrence of an ovarian Sertoli-Leydig cell tumor with a thyroid carcinoma is highly suggestive of a DICER1 syndrome. Virchows Arch. 468, 631–636 (2016).
Bethune, J., Artus-Revel, C. G. & Filipowicz, W. Kinetic analysis reveals successive steps leading to miRNA-mediated silencing in mammalian cells. EMBO Rep. 13, 716–723 (2012).
Bazzini, A. A., Lee, M. T. & Giraldez, A. J. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336, 233–237 (2012).
Djuranovic, S., Nahvi, A. & Green, R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237–240 (2012).
Schirle, N. T. & MacRae, I. J. The crystal structure of human Argonaute2. Science 336, 1037–1040 (2012).
Pfaff, J. et al. Structural features of Argonaute-GW182 protein interactions. Proc. Natl Acad. Sci. USA 110, E3770–E3779 (2013).
Jonas, S. & Izaurralde, E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet. 16, 421–433 (2015).
Chen, Y. et al. A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Mol. Cell 54, 737–750 (2014).
Mathys, H. et al. Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression. Mol. Cell 54, 751–765 (2014).
Ozgur, S. et al. Structure of a human 4E-T/DDX6/CNOT1 complex reveals the different interplay of DDX6-binding proteins with the CCR4-NOT complex. Cell Rep. 13, 703–711 (2015).
Schirle, N. T., Sheu-Gruttadauria, J. & MacRae, I. J. Structural basis for microRNA targeting. Science 346, 608–613 (2014).
Nowak, J. S., Choudhury, N. R., de Lima Alves, F., Rappsilber, J. & Michlewski, G. Lin28a regulates neuronal differentiation and controls miR-9 production. Nat. Commun. 5, 3687 (2014).
Towbin, H. et al. Systematic screens of proteins binding to synthetic microRNA precursors. Nucleic Acids Res. 41, e47 (2013).
Heale, B. S., Keegan, L. P. & O’Connell, M. A. The effect of RNA editing and ADARs on miRNA biogenesis and function. Adv. Exp. Med. Biol. 700, 76–84 (2011).
Choudhury, N. R. et al. Trim25 is an RNA-specific activator of Lin28a/TuT4-mediated uridylation. Cell Rep. 9, 1265–1272 (2014).
Davis, B. N., Hilyard, A. C., Lagna, G. & Hata, A. SMAD proteins control DROSHA-mediated microRNA maturation. Nature 454, 56–61 (2008).
Suzuki, H. I. et al. Modulation of microRNA processing by p53. Nature 460, 529–533 (2009).
Wu, H. et al. A splicing-independent function of SF2/ASF in microRNA processing. Mol. Cell 38, 67–77 (2010).
Yang, W. et al. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat. Struct. Mol. Biol. 13, 13–21 (2006).
Rau, F. et al. Misregulation of miR-1 processing is associated with heart defects in myotonic dystrophy. Nat. Struct. Mol. Biol. 18, 840–845 (2011).
Morlando, M. et al. FUS stimulates microRNA biogenesis by facilitating co-transcriptional Drosha recruitment. EMBO J. 31, 4502–4510 (2012).
Pilotte, J., Dupont-Versteegden, E. E. & Vanderklish, P. W. Widespread regulation of miRNA biogenesis at the Dicer step by the cold-inducible RNA-binding protein, RBM3. PLOS One 6, e28446 (2011).
Suzuki, H. I. et al. MCPIP1 ribonuclease antagonizes dicer and terminates microRNA biogenesis through precursor microRNA degradation. Mol. Cell 44, 424–436 (2011).
Kawai, S. & Amano, A. BRCA1 regulates microRNA biogenesis via the DROSHA microprocessor complex. J. Cell Biol. 197, 201–208 (2012).
Xhemalce, B., Robson, S. C. & Kouzarides, T. Human RNA methyltransferase BCDIN3D regulates microRNA processing. Cell 151, 278–288 (2012).
Higuchi, T. et al. Suppression of microRNA-7 (miR-7) biogenesis by Nuclear Factor 90-Nuclear Factor 45 Complex (NF90-NF45) controls cell proliferation in hepatocellular carcinoma. J. Biol. Chem. 291, 21074–21084 (2016).
Chen, Y. et al. Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer. Nucleic Acids Res. 44, 4381–4395 (2016).
Zhang, H. et al. XRN2 promotes EMT and metastasis through regulating maturation of miR-10a. Oncogene 36, 3925–3933 (2017).
Xiong, X. P., Vogler, G., Kurthkoti, K., Samsonova, A. & Zhou, R. SmD1 modulates the miRNA pathway independently of its pre-mRNA splicing function. PLOS Genet. 11, e1005475 (2015).
Jiang, L. et al. NEAT1 scaffolds RNA-binding proteins and the microprocessor to globally enhance pri-miRNA processing. Nat. Struct. Mol. Biol. 24, 816–824 (2017).
Liz, J. et al. Regulation of pri-miRNA processing by a long noncoding RNA transcribed from an ultraconserved region. Mol. Cell 55, 138–147 (2014).
The authors apologize to those whose work was not included or cited owing to space constraints. The authors’ research is supported by grants from the European Research Council (ERC) (‘moreRNA’ 930806), the Deutsche Forschungsgemeinschaft (DFG) (FOR2127, SFB960 and SPP1935) and the Bavarian Research Network for Molecular Biosystems (BioSysNet).
Nature Reviews Molecular Cell Biology thanks W. Filipowicz, G. Michlewski and the other anonymous reviewer(s) for their contribution to the peer review of this work.
(AGO). A large family of proteins involved in small-RNA-guided gene silencing. Argonaute proteins are highly conserved and found in Eukarya, Archaea and Bacteria.
(PAZ). A domain named after the PIWI, Argonaute and Zwille proteins that is characteristic of Argonaute proteins and also found in some Dicer enzymes. The domain anchors the 3ʹend of the bound small RNA.
- P element-induced wimpy testes
(PIWI). A domain characteristic of Argonaute proteins. PIWI domains are structurally similar to RNase H, and some possess catalytic activity.
- Electron microscopy density maps
In electron microscopy, higher electron density leads to stronger absorption and scattering by interaction of the beam with electrons of the sample. Electron density maps are a 3D reconstruction of the signal, which is the basis for structure model building.
- RNA exosome
An abundant 3ʹ– 5ʹ exoribonuclease complex that is found in all Eukarya as well as in some Archaea.
- Crosslinking and immunoprecipitation
A method used to identify RNA sites that are bound by proteins.
- Import receptor
A protein that transports another protein or RNA molecule (cargo) from the cytoplasm into the nucleus.
The release of the 2ʹ−5ʹ phosphodiester linkage of the intron lariat during pre-mRNA splicing.
- Intron lariat
A lariat structure that is formed in the intron during splicing by covalent linkage of the 5ʹ end of the intron and a 2ʹ hydroxyl group of an intronic internal adenosine.