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Mini Review

Post-transcriptional control of miRNA abundance in Arabidopsis

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Pages 1443-1446 | Published online: 07 Sep 2012

References

  • Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002; 297:2053 - 6; 10.1126/science.1076311; PMID: 12242443
  • Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev 2002; 16:1616 - 26; 10.1101/gad.1004402; PMID: 12101121
  • Park W, Li J, Song R, Messing J, Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana.. Curr Biol 2002; 12:1484 - 95; 10.1016/S0960-9822(02)01017-5; PMID: 12225663
  • Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J 2006; 46:243 - 59; 10.1111/j.1365-313X.2006.02697.x; PMID: 16623887
  • Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell 2002; 110:513 - 20; 10.1016/S0092-8674(02)00863-2; PMID: 12202040
  • Khraiwesh B, Zhu JK, Zhu J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 2012; 1819:137-48.
  • Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004; 23:4051 - 60; 10.1038/sj.emboj.7600385; PMID: 15372072
  • Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. Expression of Arabidopsis MIRNA genes. Plant Physiol 2005; 138:2145 - 54; 10.1104/pp.105.062943; PMID: 16040653
  • Chen X. Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 2009; 25:21 - 44; 10.1146/annurev.cellbio.042308.113417; PMID: 19575669
  • Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009; 136:669 - 87; 10.1016/j.cell.2009.01.046; PMID: 19239888
  • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006; 20:3407 - 25; 10.1101/gad.1476406; PMID: 17182867
  • Baumberger N, Baulcombe DC. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A 2005; 102:11928 - 33; 10.1073/pnas.0505461102; PMID: 16081530
  • Qi Y, Denli AM, Hannon GJ. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell 2005; 19:421 - 8; 10.1016/j.molcel.2005.06.014; PMID: 16061187
  • Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM. The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 2009; 15:2219 - 35; 10.1261/rna.1646909; PMID: 19861421
  • Smith MR, Willmann MR, Wu G, Berardini TZ, Möller B, Weijers D, et al. Cyclophilin 40 is required for microRNA activity in Arabidopsis. Proc Natl Acad Sci U S A 2009; 106:5424 - 9; 10.1073/pnas.0812729106; PMID: 19289849
  • Iki T, Yoshikawa M, Meshi T, Ishikawa M. Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants. EMBO J 2012; 31:267 - 78; 10.1038/emboj.2011.395; PMID: 22045333
  • Earley KW, Poethig RS. Binding of the cyclophilin 40 ortholog SQUINT to Hsp90 protein is required for SQUINT function in Arabidopsis. J Biol Chem 2011; 286:38184 - 9; 10.1074/jbc.M111.290130; PMID: 21908611
  • Lobbes D, Rallapalli G, Schmidt DD, Martin C, Clarke J. SERRATE: a new player on the plant microRNA scene. EMBO Rep 2006; 7:1052 - 8; 10.1038/sj.embor.7400806; PMID: 16977334
  • Yang L, Liu Z, Lu F, Dong A, Huang H. SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J 2006; 47:841 - 50; 10.1111/j.1365-313X.2006.02835.x; PMID: 16889646
  • Han MH, 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 U S A 2004; 101:1093 - 8; 10.1073/pnas.0307969100; PMID: 14722360
  • Fang Y, Spector DL. Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr Biol 2007; 17:818 - 23; 10.1016/j.cub.2007.04.005; PMID: 17442570
  • Song L, Han MH, Lesicka J, Fedoroff N. Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body. Proc Natl Acad Sci U S A 2007; 104:5437 - 42; 10.1073/pnas.0701061104; PMID: 17369351
  • Fujioka Y, Utsumi M, Ohba Y, Watanabe Y. Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis. Plant Cell Physiol 2007; 48:1243 - 53; 10.1093/pcp/pcm099; PMID: 17675322
  • Dong Z, Han MH, Fedoroff N. The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci U S A 2008; 105:9970 - 5; 10.1073/pnas.0803356105; PMID: 18632569
  • Liu C, Axtell MJ, Fedoroff NV. The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis. Plant Physiol 2012; 159:748 - 58; 10.1104/pp.112.193508; PMID: 22474216
  • Werner S, Wollmann H, Schneeberger K, Weigel D. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana.. Curr Biol 2010; 20:42 - 8; 10.1016/j.cub.2009.10.073; PMID: 20015654
  • Mateos JL, Bologna NG, Chorostecki U, Palatnik JF. Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor. Curr Biol 2010; 20:49 - 54; 10.1016/j.cub.2009.10.072; PMID: 20005105
  • Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 2009; 10:126 - 39; 10.1038/nrm2632; PMID: 19165215
  • Cuperus JT, Montgomery TA, Fahlgren N, Burke RT, Townsend T, Sullivan CM, et al. Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc Natl Acad Sci U S A 2010; 107:466 - 71; 10.1073/pnas.0913203107; PMID: 20018656
  • Song L, Axtell MJ, Fedoroff NV. RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Curr Biol 2010; 20:37 - 41; 10.1016/j.cub.2009.10.076; PMID: 20015653
  • Addo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ. Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA 2009; 15:2112 - 21; 10.1261/rna.1774909; PMID: 19850910
  • Bologna NG, Mateos JL, Bresso EG, Palatnik JF. A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J 2009; 28:3646 - 56; 10.1038/emboj.2009.292; PMID: 19816405
  • Zhang W, Gao S, Zhou X, Xia J, Chellappan P, Zhou X, et al. Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 2010; 11:R81; 10.1186/gb-2010-11-8-r81; PMID: 20696037
  • Laubinger S, Zeller G, Henz SR, Buechel S, Sachsenberg T, Wang JW, et al. Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. Proc Natl Acad Sci U S A 2010; 107:17466 - 73; 10.1073/pnas.1012891107; PMID: 20870966
  • Xie Z, Kasschau KD, Carrington JC. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol 2003; 13:784 - 9; 10.1016/S0960-9822(03)00281-1; PMID: 12725739
  • Pouch-Pélissier MN, Pélissier T, Elmayan T, Vaucheret H, Boko D, Jantsch MF, et al. SINE RNA induces severe developmental defects in Arabidopsis thaliana and interacts with HYL1 (DRB1), a key member of the DCL1 complex. PLoS Genet 2008; 4:e1000096; 10.1371/journal.pgen.1000096; PMID: 18551175
  • Ren G, Xie M, Dou Y, Zhang S, Zhang C, Yu B. Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci U S A 2012; 109:12817 - 21; 10.1073/pnas.1204915109; PMID: 22802657
  • Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M, et al. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci U S A 2008; 105:10073 - 8; 10.1073/pnas.0804218105; PMID: 18632581
  • Calderon-Villalobos LI, Kuhnle C, Dohmann EM, Li H, Bevan M, Schwechheimer C. The evolutionarily conserved TOUGH protein is required for proper development of Arabidopsis thaliana. Plant Cell 2005; 17:2473 - 85; 10.1105/tpc.105.031302; PMID: 16024589
  • Hajheidari M, Farrona S, Huettel B, Koncz Z, Koncz C. CDKF;1 and CDKD protein kinases regulate phosphorylation of serine residues in the C-terminal domain of Arabidopsis RNA polymerase II. Plant Cell 2012; 24:1626 - 42; 10.1105/tpc.112.096834; PMID: 22547781
  • Kim S, Yang JY, Xu J, Jang IC, Prigge MJ, Chua NH. Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol 2008; 49:1634 - 44; 10.1093/pcp/pcn146; PMID: 18829588
  • Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Rätsch G, et al. Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2008; 105:8795 - 800; 10.1073/pnas.0802493105; PMID: 18550839
  • Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, et al. Methylation as a crucial step in plant microRNA biogenesis. Science 2005; 307:932 - 5; 10.1126/science.1107130; PMID: 15705854
  • Yang Z, Ebright YW, Yu B, Chen X. 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 2006; 34:667 - 75; 10.1093/nar/gkj474; PMID: 16449203
  • Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, Ma JB. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 2009; 461:823 - 7; 10.1038/nature08433; PMID: 19812675
  • 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; 15:1501 - 7; 10.1016/j.cub.2005.07.029; PMID: 16111943
  • Yu B, Bi L, Zhai J, Agarwal M, Li S, Wu Q, et al. siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Res 2010; 38:5844 - 50; 10.1093/nar/gkq348; PMID: 20448024
  • Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh TT, Meyers BC, et al. The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol 2012; 22:689 - 94; 10.1016/j.cub.2012.02.051; PMID: 22464194
  • Ren G, Chen X, Yu B. Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis. Curr Biol 2012; 22:695 - 700; 10.1016/j.cub.2012.02.052; PMID: 22464191
  • Ibrahim F, Rymarquis LA, Kim EJ, Becker J, Balassa E, Green PJ, et al. Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas. Proc Natl Acad Sci U S A 2010; 107:3906 - 11; 10.1073/pnas.0912632107; PMID: 20142471
  • Ibrahim F, Rohr J, Jeong WJ, Hesson J, Cerutti H. Untemplated oligoadenylation promotes degradation of RISC-cleaved transcripts. Science 2006; 314:1893; 10.1126/science.1135268; PMID: 17185594
  • Ramachandran V, Chen X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 2008; 321:1490 - 2; 10.1126/science.1163728; PMID: 18787168
  • Han BW, Hung JH, Weng Z, Zamore PD, Ameres SL. The 3′-to-5′ exoribonuclease Nibbler shapes the 3′ ends of microRNAs bound to Drosophila Argonaute1. Curr Biol 2011; 21:1878 - 87; 10.1016/j.cub.2011.09.034; PMID: 22055293
  • Liu N, Abe M, Sabin LR, Hendriks GJ, Naqvi AS, Yu Z, et al. The exoribonuclease Nibbler controls 3′ end processing of microRNAs in Drosophila. Curr Biol 2011; 21:1888 - 93; 10.1016/j.cub.2011.10.006; PMID: 22055292
  • Darnell RB. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA 2010; 1:266 - 86; 10.1002/wrna.31; PMID: 21935890

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