Abstract
miRNAs play important regulatory roles in various plant metabolic pathways. Similar to any key regulator, miRNA genes are under a variety of transcriptional and post-transcriptional controls. Another layer of this regulation is provided by the regulation of Microprocessor protein components as well as their interactions with other regulatory proteins. When in cytoplasm, miRNA mode of action and turnover is also influenced by various protein partners that either bind directly to the miRNA or interact with them indirectly. We put together currently available data to provide a comprehensive overview regarding miRNA biogenesis, mode of action, and turnover in plants.
Aleksandra Grabowska and Susheel Sagar Bhat contributed equally to this work.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aceto S, Sica M, De Paolo S et al (2014) The analysis of the inflorescence miRNome of the Orchid Orchis italica reveals a DEF-like MADS-box gene as a new miRNA target. PLoS ONE 9:e97839
Achkar NP, Cho SK, Poulsen C et al (2018) A quick HYL1-dependent reactivation of microRNA production is required for a proper developmental response after extended periods of light deprivation. Dev Cell 46:236–247.e6. https://doi.org/10.1016/j.devcel.2018.06.014
Alarcón CR, Lee H, Goodarzi H et al (2015) N6-methyladenosine marks primary microRNAs for processing. Nature 519:482–485. https://doi.org/10.1038/nature14281
Allen E, Xie Z, Gustafson AM et al (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36:1282–1290. https://doi.org/10.1038/ng1478
Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15:2730 LP–2741. https://doi.org/10.1105/tpc.016238
Baek D, Park HC, Kim MC, Yun D-J (2013) The role of Arabidopsis MYB2 in miR399f-mediated phosphate-starvation response. Plant Signal Behav 8:e23488. https://doi.org/10.4161/psb.23488
Baldrich P, Hsing Y-IC, San Segundo B (2016) Genome-wide analysis of polycistronic microRNAs in cultivated and wild rice. Genome Biol Evol 8:1104–1114. https://doi.org/10.1093/gbe/evw062
Barciszewska-Pacak M, Milanowska K, Knop K et al (2015a) Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses. Front Plant Sci 6:1–14. https://doi.org/10.3389/fpls.2015.00410
Barciszewska-Pacak M, Milanowska K, Knop K et al (2015b) Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses. Front Plant Sci 6:410. https://doi.org/10.3389/fpls.2015.00410
Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci 102:11928–11933. https://doi.org/10.1073/pnas.0505461102
Bhagat PK, Verma D, Badmi R, Sinha AK (2018) Dynamic regulation of HYL1 provides new insights into its multifaceted role in Arabidopsis. bioRxiv 396861. https://doi.org/10.1101/396861
Bhat SS, Bielewicz D, Grzelak N et al (2019) mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana. bioRxiv 557900. https://doi.org/10.1101/557900
Bielewicz D, Kalak M, Kalyna M et al (2013) Introns of plant pri-miRNAs enhance miRNA biogenesis. EMBO Rep 14:622–628. https://doi.org/10.1038/embor.2013.62
Bollman KM, Aukerman MJ, Park M-Y et al (2003) HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 130:1493–1504
Bologna NG, Mateos JL, Bresso EG, Palatnik JF (2009) A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J 28:3646–3656. https://doi.org/10.1038/emboj.2009.292
Bologna NG, Schapire AL, Zhai J et al (2013) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Res 23:1675–1689. https://doi.org/10.1101/gr.153387.112
Bologna NG, Iselin R, Abriata LA et al (2018) Short article nucleo-cytosolic shuttling of ARGONAUTE1 prompts a revised model of the plant microRNA short article nucleo-cytosolic shuttling of ARGONAUTE1 prompts a revised model of the plant microRNA pathway. Mol Cell 69:1–11. https://doi.org/10.1016/j.molcel.2018.01.007
Branscheid A, Marchais A, Schott G et al (2015) SKI2 mediates degradation of RISC 5′-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis. Nucleic Acids Res 43:10975–10988. https://doi.org/10.1093/nar/gkv1014
Brodersen P, Crete P, Robaglia C et al (2009) Biochemical evidence for translational repression by arabidopsis microRNAs. Plant Cell Online 21:1762–1768. https://doi.org/10.1105/tpc.108.063412
Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M et al (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190. https://doi.org/10.1126/science.1159151
Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44. https://doi.org/10.1146/annurev.cellbio.042308.113417
Brown JWS, Marshall DF, Echeverria M (2008) Intronic noncoding RNAs and splicing. Trends Plant Sci 13:335–342. https://doi.org/10.1016/j.tplants.2008.04.010
Chen J, Li WX, Xie D et al (2004) Viral virulence protein suppresses RNA silencing-mediated defense but upregulates the role of microRNA in host gene expression. Plant Cell 16:1302–1313. https://doi.org/10.1105/tpc.018986
Cho SK, Ben Chaabane S, Shah P et al (2014) COP1 E3 ligase protects HYL1 to retain microRNA biogenesis. Nat Commun 5:5867
de Lorenzo L, Sorenson R, Bailey-Serres J, Hunt AG (2017) Noncanonical alternative polyadenylation contributes to gene regulation in response to hypoxia. Plant Cell 29:1262–1277. https://doi.org/10.1105/tpc.16.00746
Devers EA, Branscheid A, May P, Krajinski F (2011) Stars and symbiosis: microRNA- and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis. Plant Physiol 156:1990 LP–2010. https://doi.org/10.1104/pp.111.172627
Eamens AL, Smith NA, Curtin SJ, et al (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. 2219–2235. https://doi.org/10.1261/rna.1646909
Eamens AL, Kim KW, Waterhouse PM (2012) DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana. Plant Signal Behav 7:1224–1229. https://doi.org/10.4161/psb.21518
Fang Y, Spector DL (2007) Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr Biol 17:818–823. https://doi.org/10.1016/j.cub.2007.04.005
Fang X, Cui Y, Li Y, Qi Y (2015) Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis. Nat Plants 1:15075. https://doi.org/10.1038/nplants.2015.75
Fang X, Zhao G, Zhang S et al (2019) Chloroplast-to-nucleus signaling regulates microRNA biogenesis in Arabidopsis. Dev Cell 48:371–382.e4. https://doi.org/10.1016/j.devcel.2018.11.046
Franco-Zorrilla JM, Valli A, Todesco M et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39:1033–1037. https://doi.org/10.1038/ng2079
Gandikota M, Birkenbihl RP, Hohmann S et al (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 49:683–693. https://doi.org/10.1111/j.1365-313X.2006.02983.x
Gingras A-C, Caballero M, Zarske M et al (2005) A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity. Mol Cell Proteomics 4:1725–1740. https://doi.org/10.1074/mcp.M500231-MCP200
Hernandez-Lagana E, Rodriguez-Leal D, Lua J, Vielle-Calzada J-P (2016) A multigenic network of ARGONAUTE4 clade members controls early megaspore formation in Arabidopsis. Genetics 204:1045–1056. https://doi.org/10.1534/genetics.116.188151
Iki T, Yoshikawa M, Nishikiori M et al (2010) In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90. Mol Cell 39:282–291. https://doi.org/10.1016/j.molcel.2010.05.014
Ivashuta S, Banks IR, Wiggins BE et al (2011) Regulation of gene expression in plants through miRNA inactivation. PLoS ONE 6:e21330. https://doi.org/10.1371/journal.pone.0021330
Jeong IS, Aksoy E, Fukudome A et al (2013) Arabidopsis C-terminal domain phosphatase-like 1 functions in miRNA accumulation and DNA methylation. PLoS ONE 8:e74739. https://doi.org/10.1371/journal.pone.0074739
Ji L, Liu X, Yan J et al (2011) ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis. PLoS Genet 7:e1001358. https://doi.org/10.1371/journal.pgen.1001358
Jia F, Rock CD (2013) Jacalin lectin At5g28520 is regulated by ABA and miR846. Plant Signal Behav 8:e24563. https://doi.org/10.4161/psb.24563
Jia L, Zhang D, Qi X et al (2014) Identification of the conserved and novel miRNAs in Mulberry by high-throughput sequencing. PLoS ONE 9:e104409. https://doi.org/10.1371/journal.pone.0104409
Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799. https://doi.org/10.1016/j.molcel.2004.05.027
Jouannet V, Moreno AB, Elmayan T et al (2012) Cytoplasmic Arabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis. EMBO J 31:1704–1713. https://doi.org/10.1038/emboj.2012.20
Kataya ARA, Creighton MT, Napitupulu TP et al (2017) PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses. PLoS ONE 12:e0180478. https://doi.org/10.1371/journal.pone.0180478
Kim YJ, Zheng B, Yu Y et al (2011) The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J 30:814–822. https://doi.org/10.1038/emboj.2011.3
Knop K, Stepien A, Barciszewska-Pacak M et al (2017) Active 5′ splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes. Nucleic Acids Res 45:2757–2775. https://doi.org/10.1093/nar/gkw895
Kruszka K, Pieczynski M, Windels D et al (2012) Role of microRNAs and other sRNAs of plants in their changing environments. J Plant Physiol 169:1664–1672. https://doi.org/10.1016/j.jplph.2012.03.009
Kurihara Y (2005) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12:206–212. https://doi.org/10.1261/rna.2146906
Kurihara Y, Watanabe Y (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci U S A 101:12753–12758. https://doi.org/10.1073/pnas.0403115101
Laubinger S, Sachsenberg T, Zeller G et al (2008) Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci 105:8795–8800. https://doi.org/10.1073/pnas.0802493105
Lauressergues D, Couzigou J-M, Clemente HS et al (2015) Primary transcripts of microRNAs encode regulatory peptides. Nature 520:90–93. https://doi.org/10.1038/nature14346
Lee Y, Kim M, Han J et al (2004) microRNA genes are transcribed by RNA polymerase II. EMBO J 23:4051–4060. https://doi.org/10.1038/sj.emboj.7600385
Li J, Yang Z, Yu B, et al (2005) Methylation Protects miRNAs and siRNAs from a 3′- end uridylation activity in Arabidopsis. 15:1501–1507. https://doi.org/10.1016/j.cub.2005.07.029
Li S, Liu L, Zhuang X et al (2013) microRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153:562–574. https://doi.org/10.1016/j.cell.2013.04.005
Liu D, Song Y, Chen Z, Yu D (2009) Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiol Plant 136:223–236. https://doi.org/10.1111/j.1399-3054.2009.01229.x
Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053–2056. https://doi.org/10.1126/science.1076311
Lobbes D, Rallapalli G, Schmidt DD et al (2006) SERRATE: a new player on the plant microRNA scene. EMBO Rep 7:1052–1058. https://doi.org/10.1038/sj.embor.7400806
Lu S, Sun Y-H, Chiang VL (2009) Adenylation of plant miRNAs. Nucleic Acids Res 37:1878–1885. https://doi.org/10.1093/nar/gkp031
Lund E, Guttinger S, Calado A et al (2004) Nuclear export of microRNA precursors. Science 303:95–98. https://doi.org/10.1126/science.1090599
Maldonado-Bonilla LD (2014) Composition and function of P bodies in Arabidopsis thaliana. Front Plant Sci 5:201. https://doi.org/10.3389/fpls.2014.00201
Manavella PA, Hagmann J, Ott F et al (2012) Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151:859–870. https://doi.org/10.1016/j.cell.2012.09.039
Maunoury N, Vaucheret H (2011) AGO1 and AGO2 act redundantly in miR408-mediated Plantacyanin regulation. PLoS ONE 6:e28729. https://doi.org/10.1371/journal.pone.0028729
Megraw M, Baev V, Rusinov V et al (2006) microRNA promoter element discovery in Arabidopsis. RNA 12:1612–1619. https://doi.org/10.1261/rna.130506
Merchan F, Boualem A, Crespi M, Frugier F (2009) Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins. Genome Biol 10:R136. https://doi.org/10.1186/gb-2009-10-12-r136
Mi S, Cai T, Hu Y et al (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133:116–127. https://doi.org/10.1016/j.cell.2008.02.034
Montgomery TA, Howell MD, Cuperus JT et al (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128–141. https://doi.org/10.1016/j.cell.2008.02.033
Motomura K, Le QT, Kumakura N et al (2012) The role of decapping proteins in the miRNA accumulation in Arabidopsis thaliana. RNA Biol 9:644–652. https://doi.org/10.4161/rna.19877
Mount SM, Pettersson I, Hinterberger M et al (1983) The U1 small nuclear RNA-protein complex selectively binds a 5′ splice site in vitro. Cell 33:509–518. https://doi.org/10.1016/0092-8674(83)90432-4
Niu D, Lii YE, Chellappan P et al (2016) miRNA863-3p sequentially targets negative immune regulator ARLPKs and positive regulator SERRATE upon bacterial infection. Nat Commun 7:11324. https://doi.org/10.1038/ncomms11324
Palatnik JF, Allen E, Wu X et al (2003) Control of leaf morphogenesis by microRNAs. Nature 425:257–263. https://doi.org/10.1038/nature01958
Palatnik JF, Wollmann H, Schommer C et al (2007) Sequence and Expression differences underlie functional specialization of Arabidopsis MicroRNAs miR159 and miR319. Dev Cell 13:115–125. https://doi.org/10.1016/j.devcel.2007.04.012
Park MY, Wu G, Gonzalez-Sulser A et al (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci U S A 102:3691–3696. https://doi.org/10.1073/pnas.0405570102
Peng T, Lv Q, Zhang J et al (2011) Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa). J Exp Bot 62:4943–4954. https://doi.org/10.1093/jxb/err205
Pujol G, Baskin TI, Casamayor A et al (2000) The Arabidopsis thaliana PPX/PP4 phosphatases: molecular cloning and structural organization of the genes and immunolocalization of the proteins to plastids. Plant Mol Biol 44:499–511
Qu F, Ye X, Morris TJ (2008) Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A 105:14732–14737. https://doi.org/10.1073/pnas.0805760105
Raghuram B, Sheikh AH, Rustagi Y, Sinha AK (2015) microRNA biogenesis factor DRB1 is a phosphorylation target of mitogen activated protein kinase MPK3 in both rice and Arabidopsis. FEBS J 282:521–536. https://doi.org/10.1111/febs.13159
Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20:3407–3425. https://doi.org/10.1101/gad.1476406
Ramachandran V, Chen X (2008) Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321:1490–1492. https://doi.org/10.1126/science.1163728
Reinhart BJ, Weinstein EG, Rhoades MW et al (2002) microRNAs in plants. Genes Dev 16:1616–1626. https://doi.org/10.1101/gad.1004402
Reis RS, Hart-Smith G, Eamens AL et al (2015a) Gene regulation by translational inhibition is determined by Dicer partnering proteins. Nat Plants 1:1–6. https://doi.org/10.1038/nplants.2014.27
Reis RS, Hart-Smith G, Eamens AL et al (2015b) microRNA Regulatory Mechanisms Play Different Roles in Arabidopsis. J Proteome Res 14:4743–4751. https://doi.org/10.1021/acs.jproteome.5b00616
Ren G, Chen X, Yu B (2012a) Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis. Curr Biol 22:695–700. https://doi.org/10.1016/j.cub.2012.02.052
Ren G, Xie M, Dou Y et al (2012b) Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci U S A 109:12817–12821. https://doi.org/10.1073/pnas.1204915109
Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25:2383–2399. https://doi.org/10.1105/tpc.113.113159
Rosbash M, Seraphin B (1991) Who’s on first? The U1 snRNP-5′ splice site interaction and splicing. Trends Biochem Sci 16:187–190
Schwab R, Speth C, Laubinger S, Voinnet O (2013) Enhanced microRNA accumulation through stemloop-adjacent introns. EMBO Rep 14:615–621. https://doi.org/10.1038/embor.2013.58
Shen Y, Ji G, Haas BJ et al (2008) Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation. Nucleic Acids Res 36:3150–3161. https://doi.org/10.1093/nar/gkn158
Shomron N, Levy C (2009) MicroRNA-biogenesis and pre-mRNA splicing crosstalk. J Biomed Biotechnol 2009:594678. https://doi.org/10.1155/2009/594678
Song L, Axtell MJ, Fedoroff NV (2010) RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Curr Biol 20:37–41. https://doi.org/10.1016/j.cub.2009.10.076
Souret FF, Kastenmayer JP, Green PJ (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15:173–183. https://doi.org/10.1016/j.molcel.2004.06.006
Stepien A, Knop K, Dolata J et al (2017) Post transcriptional coordination of splicing and miRNA biogenesis in plants. Wiley Interdiscip Rev RNA 8:e1403. https://doi.org/10.1002/wrna.1403
Su C, Li Z, Cheng J et al (2017) The protein phosphatase 4 and SMEK1 complex dephosphorylates HYL1 to promote miRNA biogenesis by antagonizing the MAPK cascade in Arabidopsis. Dev Cell 41:527–539.e5. https://doi.org/10.1016/j.devcel.2017.05.008
Świda-Barteczka A, Krieger-Liszkay A, Bilger W et al (2018) The plastid-nucleus located DNA/RNA binding protein WHIRLY1 regulates microRNA-levels during stress in barley (Hordeum vulgare L.). RNA Biol 15:886–891. https://doi.org/10.1080/15476286.2018.1481695
Takeda A, Iwasaki S, Watanabe T et al (2008) The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol 49:493–500. https://doi.org/10.1093/pcp/pcn043
Talmor-Neiman M, Stav R, Frank W et al (2006) Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss. Plant J 47:25–37. https://doi.org/10.1111/j.1365-313X.2006.02768.x
Tu B, Liu L, Xu C et al (2015) Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genet 11:e1005119. https://doi.org/10.1371/journal.pgen.1005119
Vaucheret H (2008) Plant ARGONAUTES. Trends Plant Sci 13:350–358. https://doi.org/10.1016/j.tplants.2008.04.007
Vaucheret H, Vazquez F, Crété P, Bartel DP (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18:1187–1197. https://doi.org/10.1101/gad.1201404.called
Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687. https://doi.org/10.1016/j.cell.2009.01.046
Wang F, Perry SE (2013) Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development. Plant Physiol 161:1251–1264. https://doi.org/10.1104/pp.112.212282
Wang L, Song X, Gu L et al (2013) NOT2 proteins promote polymerase II-dependent transcription and interact with multiple microRNA biogenesis factors in Arabidopsis. Plant Cell 25:715–727. https://doi.org/10.1105/tpc.112.105882
Wang X, Zhang S, Dou Y et al (2015) Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3′ tailing of small RNAs in Arabidopsis. PLoS Genet 11:e1005091. https://doi.org/10.1371/journal.pgen.1005091
Wang X, Wang Y, Dou Y, et al (2018a) Degradation of unmethylated miRNA/miRNA*s by a DEDDy-type 3′ to 5′ exoribonuclease Atrimmer 2 in Arabidopsis. Proc Natl Acad Sci U S A 201721917. https://doi.org/10.1073/pnas.1721917115
Wang Z, Ma Z, Castillo-González C et al (2018b) SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production. Nature 557:516–521. https://doi.org/10.1038/s41586-018-0135-x
Wang S, Quan L, Li S et al (2019) The PROTEIN PHOSPHATASE4 complex promotes transcription and processing of primary microRNAs in Arabidopsis. Plant Cell 31:486–501. https://doi.org/10.1105/tpc.18.00556
Werner S, Wollmann H, Schneeberger K, Weigel D (2010) Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr Biol 20:42–48. https://doi.org/10.1016/j.cub.2009.10.073
Wu G, Poethig RS (2006) Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133:3539 LP–3547. https://doi.org/10.1242/dev.02521
Wu H-J, Wang Z-M, Wang M, Wang X-J (2013a) Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol 161:1875–1884. https://doi.org/10.1104/pp.113.215962
Wu X, Shi Y, Li J et al (2013b) A role for the RNA-binding protein MOS2 in microRNA maturation in Arabidopsis. Cell Res 23:645–657. https://doi.org/10.1038/cr.2013.23
Wyman SK, Knouf EC, Parkin RK et al (2011) Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res 21:1450–1461. https://doi.org/10.1101/gr.118059.110
Xie Z (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol 138:2145–2154. https://doi.org/10.1104/pp.105.062943
Xie Z, Kasschau KD, Carrington JC (2003) Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol 13:784–789
Yamasaki H, Hayashi M, Fukazawa M et al (2009) SQUAMOSA promoter binding Protein-Like7 is a central regulator for copper homeostasis in Arabidopsis. Plant Cell 21:347–361. https://doi.org/10.1105/tpc.108.060137
Yan J, Wang P, Wang B et al (2017) The SnRK2 kinases modulate miRNA accumulation in Arabidopsis. PLoS Genet 13:e1006753. https://doi.org/10.1371/journal.pgen.1006753
Yan J, Zhang H, Zheng Y, Ding Y (2015) Comparative expression profiling of miRNAs between the cytoplasmic male sterile line MeixiangA and its maintainer line MeixiangB during rice anther development. Planta 241:109–123. https://doi.org/10.1007/s00425-014-2167-2
Yang Z, Ebright YW, Yu B, Chen X (2006) HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res 34:667–675. https://doi.org/10.1093/nar/gkj474
Yang L, Wu G, Poethig RS (2012) Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis. Proc Natl Acad Sci U S A 109:315–320. https://doi.org/10.1073/pnas.1114673109
Yant L, Mathieu J, Dinh TT et al (2010) Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell 22:2156 LP–2170. https://doi.org/10.1105/tpc.110.075606
Yu B, Yang Z, Li J et al (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307:932–935. https://doi.org/10.1126/science.1107130
Yu Y, Jia T, Chen X (2017) The “how” and “where” of plant microRNAs. New Phytol 216:1002–1017. https://doi.org/10.1111/nph.14834
Zhang L, Chia J-M, Kumari S et al (2009) A genome-wide characterization of microRNA genes in maize. PLoS Genet 5:e1000716. https://doi.org/10.1371/journal.pgen.1000716
Zhang S, Xie M, Ren G, Yu B (2013) CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts. Proc Natl Acad Sci 110:17588–17593. https://doi.org/10.1073/pnas.1310644110
Zhang J, Huang M, Liang J et al (2016) Genome-wide mining for microRNAs and their targets in Betula luminifera using high-throughput sequencing and degradome analyses. Tree Genet Genomes 12:99. https://doi.org/10.1007/s11295-016-1047-2
Zhang Z, Hu F, Sung MW et al (2017) RISC-interacting clearing 3′–5′ exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana. Elife 6:e24466. https://doi.org/10.7554/eLife.24466
Zhao Y, Yu Y, Zhai J et al (2012) The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol 22:689–694. https://doi.org/10.1016/j.cub.2012.02.051
Zhu H, Hu F, Wang R et al (2011) Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 145:242–256. https://doi.org/10.1016/j.cell.2011.03.024
Acknowledgements
This work was supported by the NCN grants: 2017/, 27/N/NZ1/0020 to SSB 2016/23/D/NZ1/00152 to DB, 2016/23/N/NZ1/00005 to AS, 2013/10/A/NZ1/00557 to AJ and 2016/23/B/NZ9/00862 to Z S-K.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Grabowska, A., Bhat, S.S., Smoczynska, A., Bielewicz, D., Jarmolowski, A., Kulinska, Z.S. (2020). Regulation of Plant microRNA Biogenesis. In: Miguel, C., Dalmay, T., Chaves, I. (eds) Plant microRNAs. Concepts and Strategies in Plant Sciences. Springer, Cham. https://doi.org/10.1007/978-3-030-35772-6_1
Download citation
DOI: https://doi.org/10.1007/978-3-030-35772-6_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-35771-9
Online ISBN: 978-3-030-35772-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)