MicroRNA Production in

Overview

Journal Front Plant Sci

Date 2023 Feb 6

PMID 36743500

Authors

Ning Ding

Bailong Zhang

Affiliations

Soon will be listed here.

Abstract

In plants, microRNAs (miRNAs) associate with ARGONAUTE (AGO) proteins and act as sequence-specific repressors of target gene expression, at the post-transcriptional level through target transcript cleavage and/or translational inhibition. MiRNAs are mainly transcribed by DNA-dependent RNA polymerase II (POL II) and processed by DICER LIKE1 (DCL1) complex into 21∼22 nucleotide (nt) long. Although the main molecular framework of miRNA biogenesis and modes of action have been established, there are still new requirements continually emerging in the recent years. The studies on the involvement factors in miRNA biogenesis indicate that miRNA biogenesis is not accomplished separately step by step, but is closely linked and dynamically regulated with each other. In this article, we will summarize the current knowledge on miRNA biogenesis, including gene transcription, primary miRNA (pri-miRNA) processing, miRNA AGO1 loading and nuclear export; and miRNA metabolism including methylation, uridylation and turnover. We will describe how miRNAs are produced and how the different steps are regulated. We hope to raise awareness that the linkage between different steps and the subcellular regulation are becoming important for the understanding of plant miRNA biogenesis and modes of action.

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References

Wang X, Zhang S, Dou Y, Zhang C, Chen X, Yu B . Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3' tailing of small RNAs in Arabidopsis. PLoS Genet. 2015; 11(4):e1005091. PMC: 4415790. DOI: 10.1371/journal.pgen.1005091. View

Li S, Xu R, Li A, Liu K, Gu L, Li M . SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis. Nucleic Acids Res. 2018; 46(17):9148-9159. PMC: 6158494. DOI: 10.1093/nar/gky591. View

Tsai H, Li Y, Hsieh W, Lin M, Ahn J, Wu S . HUA ENHANCER1 is involved in posttranscriptional regulation of positive and negative regulators in Arabidopsis photomorphogenesis. Plant Cell. 2014; 26(7):2858-72. PMC: 4145119. DOI: 10.1105/tpc.114.126722. View

Bologna N, Mateos J, Bresso E, Palatnik J . A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J. 2009; 28(23):3646-56. PMC: 2790483. DOI: 10.1038/emboj.2009.292. View

Zhu H, Hu F, Wang R, Zhou X, Sze S, Liou L . Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell. 2011; 145(2):242-56. PMC: 4124879. DOI: 10.1016/j.cell.2011.03.024. View

Chekanova J, Gregory B, Reverdatto S, Chen H, Kumar R, Hooker T . Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell. 2007; 131(7):1340-53. DOI: 10.1016/j.cell.2007.10.056. View

Fang X, Shi Y, Lu X, Chen Z, Qi Y . CMA33/XCT Regulates Small RNA Production through Modulating the Transcription of Dicer-Like Genes in Arabidopsis. Mol Plant. 2015; 8(8):1227-36. DOI: 10.1016/j.molp.2015.03.002. View

Wang W, Ye R, Xin Y, Fang X, Li C, Shi H . An importin β protein negatively regulates MicroRNA activity in Arabidopsis. Plant Cell. 2011; 23(10):3565-76. PMC: 3229135. DOI: 10.1105/tpc.111.091058. View

Souret F, Kastenmayer J, Green P . AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell. 2004; 15(2):173-83. DOI: 10.1016/j.molcel.2004.06.006. View

10.

Zhai J, Zhao Y, Simon S, Huang S, Petsch K, Arikit S . Plant microRNAs display differential 3' truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species. Plant Cell. 2013; 25(7):2417-28. PMC: 3753374. DOI: 10.1105/tpc.113.114603. View

11.

Ramachandran V, Chen X . Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science. 2008; 321(5895):1490-2. PMC: 2570778. DOI: 10.1126/science.1163728. View

12.

Iki T, Yoshikawa M, Nishikiori M, Jaudal M, Matsumoto-Yokoyama E, Mitsuhara I . In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90. Mol Cell. 2010; 39(2):282-91. DOI: 10.1016/j.molcel.2010.05.014. View

13.

Yang X, Dong W, Ren W, Zhao Q, Wu F, He Y . Cytoplasmic HYL1 modulates miRNA-mediated translational repression. Plant Cell. 2021; 33(6):1980-1996. PMC: 8290291. DOI: 10.1093/plcell/koab090. View

14.

Reis R, Hart-Smith G, Eamens A, Wilkins M, Waterhouse P . Gene regulation by translational inhibition is determined by Dicer partnering proteins. Nat Plants. 2016; 1:14027. DOI: 10.1038/nplants.2014.27. View

15.

Li J, Yang Z, Yu B, Liu J, Chen X . Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol. 2005; 15(16):1501-7. PMC: 5127709. DOI: 10.1016/j.cub.2005.07.029. View

16.

Ren G, Xie M, Zhang S, Vinovskis C, Chen X, Yu B . Methylation protects microRNAs from an AGO1-associated activity that uridylates 5' RNA fragments generated by AGO1 cleavage. Proc Natl Acad Sci U S A. 2014; 111(17):6365-70. PMC: 4035956. DOI: 10.1073/pnas.1405083111. View

17.

Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett R . Methylation as a crucial step in plant microRNA biogenesis. Science. 2005; 307(5711):932-5. PMC: 5137370. DOI: 10.1126/science.1107130. View

18.

Xu M, Hu T, Smith M, Poethig R . Epigenetic Regulation of Vegetative Phase Change in Arabidopsis. Plant Cell. 2015; 28(1):28-41. PMC: 4746683. DOI: 10.1105/tpc.15.00854. View

19.

Bajczyk M, Lange H, Bielewicz D, Szewc L, Bhat S, Dolata J . SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis. Nucleic Acids Res. 2020; 48(12):6839-6854. PMC: 7337926. DOI: 10.1093/nar/gkaa373. View

20.

Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M . The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci U S A. 2008; 105(29):10073-8. PMC: 2481372. DOI: 10.1073/pnas.0804218105. View