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The molecular characterization and function of miRNAs on mediation of target gene silencing in plants |
Chengjin GUO1, Juntao GU2, Xiaojuan LI2, Wenjing LU2, Chunying MA1, Kai XIAO1() |
1. College of Agronomy, Agricultural University of Hebei, Baoding 071001, China; 2. College of Life Science, Agricultural University of Hebei, Baoding 071001, China |
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Abstract MiRNAs belong to one type of noncoding RNAs involved in developmental regulation, genome maintenance, and defense in eukaryotes. In plants, the miRNAs are involved in many molecular interactions, including interfere with expression of mRNAs encoding factors that control developmental processes, stem cell maintenances, auxin responses, and other developmental and physiologic processes. In this paper, the molecular characterization and the functions of miRNAs on mediation of target gene silencing in plants have been overviewed. Further studies on the miRNAs will be helpful for elucidation of the molecular mechanism of post- transcriptional gene silencing in plants.
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Keywords
miRNAs
molecular characterization
RNA-induced silencing complex (RISC)
target gene
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Corresponding Author(s):
XIAO Kai,Email:xiaokai@hebau.edu.cn
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Issue Date: 05 June 2011
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|
1 |
Abelson J F, Kwan K Y, O’Roak B J, Baek D Y, Stillman A A, Morgan T M, Mathews C A, Pauls D L, Rasin M R, Gunel M, Davis N R, Ercan-Sencicek A G, Guez D H, Spertus J A, Leckman J F, Dure L S 4th, Kurlan R, Singer H S, Gilbert D L, Farhi A, Louvi A, Lifton R P, Sestan N, State M W (2005). Sequence variants in SLITRK1 are associated with Tourette’s syndrome. Science , 310(5746): 317–320 doi: 10.1126/science.1116502
|
2 |
Achard P, Herr A, Baulcombe D C, Harberd N P (2004). Modulation of floral development by a gibberellin-regulated microRNA. Development , 131(14): 3357–3365 doi: 10.1242/dev.01206
|
3 |
Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V (2005). Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res , 15(1): 78–91 doi: 10.1101/gr.2908205
|
4 |
Allen E, Xie Z, Gustafson A M, Carrington J C (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell , 121(2): 207–221
|
5 |
Allen R D, Webb R P, Schake S A (1997). Use of transgenic plants to study antioxidant defenses. Free Radic Biol Med , 23(3): 473–479 doi: 10.1016/S0891-5849(97)00107-X
|
6 |
Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein M J, Tuschl T, Margalit H (2005). Clustering and conservation patterns of human microRNAs. Nucleic Acids Res , 33(8): 2697–2706 doi: 10.1093/nar/gki567
|
7 |
Apel K, Hirt H (2004). Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol , 55(1): 373–399 doi: 10.1146/annurev.arplant.55.031903.141701
|
8 |
Aukerman M J, Sakai H (2003). Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell , 15(11): 2730–2741 doi: 10.1105/tpc.016238
|
9 |
Axtell M J, Bartel D P (2005). Antiquity of microRNAs and their targets in land plants. Plant Cell , 17(6): 1658–1673 doi: 10.1105/tpc.105.032185
|
10 |
Bartels D, Sunka R (2005). Drought and salt tolerance in plants. CRC Crit. Rev. Plant Science , 24(1): 23–58 doi: 10.1080/07352680590910410
|
11 |
Baulcombe D (2004). RNA silencing in plants. Nature , 431(7006): 356–363 doi: 10.1038/nature02874
|
12 |
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet , 37(7): 766–770 doi: 10.1038/ng1590
|
13 |
Bernstein E, Caudy A A, Hammond S M, Hannon G J (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature , 409(6818): 363–366 doi: 10.1038/35053110
|
14 |
Bonnet E, Wuyts J, Rouzé P, Van de Peer Y (2004). Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA , 101(31): 11511–11516 doi: 10.1073/pnas.0404025101
|
15 |
Brennecke J, Hipfner D R, Stark A, Russell R B, Cohen S M (2003). Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell , 113(1): 25–36
|
16 |
Brennecke J, Stark A, Russell R B, Cohen S M (2005). Principles of microRNA-target recognition. PLoS Biol , 3(3): e85 doi: 10.1371/journal.pbio.0030085
|
17 |
Cai X, Hagedorn C H, Cullen B R (2004). Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA , 10(12): 1957–1966
|
18 |
Carmell M A, Xuan Z, Zhang M Q, Hannon G J (2002). The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev , 16(21): 2733–2742 doi: 10.1101/gad.1026102
|
19 |
Carrington J C, Ambros V (2003). Role of microRNAs in plant and animal development. Science , 301(5631): 336–338 doi: 10.1126/science.1085242
|
20 |
Chen C Z, Li L, Lodish H F, Bartel D P (2004). MicroRNAs modulate hematopoietic lineage differentiation. Science , 303(5654): 83–86 doi: 10.1126/science.1091903
|
21 |
Chen K, Rajewsky N (2006). Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet , 38(12): 1452–1456 doi: 10.1038/ng1910
|
22 |
Chen X (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science , 303(5666): 2022–2025 doi: 10.1126/science.1088060
|
23 |
Chiou T J, Aung K, Lin S I, Wu C C, Chiang S F, Su C L (2006). Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. Plant Cell , 18(2): 412–421 doi: 10.1105/tpc.105.038943
|
24 |
Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibé B, Bouix J, Caiment F, Elsen J M, Eychenne F, Larzul C, Laville E, Meish F, Milenkovic D, Tobin J, Charlier C, Georges M (2006). A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet , 38(7): 813–818 doi: 10.1038/ng1810
|
25 |
Cuellar T L, McManus M T (2005). MicroRNAs and endocrine biology. J Endocrinol , 187(3): 327–332 doi: 10.1677/joe.1.06426
|
26 |
Dolan L, Janmaat K, Willemsen V, Linstead P, Poethig S, Roberts K, Scheres B (1993). Cellular organisation of the Arabidopsis thaliana root. Development , 119(1): 71–84
|
27 |
Ehrenreich I M, Purugganan M D (2008). Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiol , 146(4): 1974–1982 doi: 10.1104/pp.108.116582
|
28 |
Eulalio A, Huntzinger E, Nishihara T, Rehwinkel J, Fauser M, Izaurralde E (2009). Deadenylation is a widespread effect of miRNA regulation. RNA , 15(1): 21–32
|
29 |
Fagard M, Boutet S, Morel J B, Bellini C, Vaucheret H (2000). AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc Natl Acad Sci USA , 97(21): 11650–11654 doi: 10.1073/pnas.200217597
|
30 |
Fahlgren N, Howell M D, Kasschau K D, Chapman E J, Sullivan C M, Cumbie J S, Givan S A, Law T F, Grant S R, Dangl J L, Carrington J C, Shiu S H (2007). High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE , 2(2): e219 doi: 10.1371/journal.pone.0000219
|
31 |
Fire A, Xu S, Montgomery M K, Kostas S A, Driver S E, Mello C C (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature , 391(6669): 806–811 doi: 10.1038/35888
|
32 |
Floyd S K, Bowman J L (2004). Gene regulation: ancient microRNA target sequences in plants. Nature , 428(6982): 485–486 doi: 10.1038/428485a
|
33 |
Foyer C H, Descourvieres P, Kunert K J (1994). Protection against oxygen radicals: An important defense mechanism studied in transgenic plants. Plant Cell Environ , 17(5): 507–523 doi: 10.1111/j.1365-3040.1994.tb00146.x
|
34 |
Foyer C H, Noctor G (2005). Redox homeostasis and antioxidant signaling: a metabolic interface between stress perception and physiological responses. Plant Cell , 17(7): 1866–1875 doi: 10.1105/tpc.105.033589
|
35 |
Friedman R C, Farh K K, Burge C B, Bartel D P (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res , 19(1): 92–105 doi: 10.1101/gr.082701.108
|
36 |
Gottwein E, Cai X, Cullen B R (2006). A novel assay for viral microRNA function identifies a single nucleotide polymorphism that affects Drosha processing. J Virol , 80(11): 5321–5326 doi: 10.1128/JVI.02734-05
|
37 |
Griffiths-Jones S (2004). The microRNA registry. Nucleic Acids Res , 32(90001 Database issue): D109–D111
|
38 |
Griffiths-Jones S, Grocock R J, van Dongen S, Bateman A, Enright A J (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res , 34(90001): 140–144 doi: 10.1093/nar/gkj112
|
39 |
Grosshans H, Slack F J (2002). Micro-RNAs: small is plentiful. J Cell Biol , 156(1): 17–21 doi: 10.1083/jcb.200111033
|
40 |
Grün D, Wang Y L, Langenberger D, Gunsalus K C, Rajewsky N (2005). microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLOS Comput Biol , 1(1): e13 doi: 10.1371/journal.pcbi.0010013
|
41 |
Hammond J P, Bennett M J, Bowen H C, Broadley M R, Eastwood D C, May S T, Rahn C, Swarup R, Woolaway K E, White P J (2003). Changes in gene expression in Arabidopsis shoots during phosphate starvation and the potential for developing smart plants. Plant Physiol , 132(2): 578–596 doi: 10.1104/pp.103.020941
|
42 |
Harfe B D, McManus M T, Mansfield J H, Hornstein E, Tabin C J (2005). The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. Proc Natl Acad Sci USA , 102(31): 10898–10903 doi: 10.1073/pnas.0504834102
|
43 |
Hawkins P G, Morris K V (2008). RNA and transcriptional modulation of gene expression. Cell Cycle , 7(5): 602–607 doi: 10.4161/cc.7.5.5522
|
44 |
Hiraguri A, Itoh R, Kondo N, Nomura Y, Aizawa D, Murai Y, Koiwa H, Seki M, Shinozaki K, Fukuhara T (2005). Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana. Plant Mol Biol , 57(2): 173–188 doi: 10.1007/s11103-004-6853-5
|
45 |
Hunter C, Sun H, Poethig R S (2003). The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr Biol , 13(19): 1734–1739 doi: 10.1016/j.cub.2003.09.004
|
46 |
Jackson D, Veit B, Hake S (1994). Expression of maize KNOTTED1 related homeobox genes in the shoot apical meristem predicts patterns of morphogenesis in the vegetative shoot. Development , 120: 405–413
|
47 |
Jones-Rhoades M W, Bartel D P (2004). Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell , 14(6): 787-799 doi: 10.1016/j.molcel.2004.05.027
|
48 |
Jones-Rhoades M W, Bartel D P, Bartel B (2006). MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol , 57(1): 19–53 doi: 10.1146/annurev.arplant.57.032905.105218
|
49 |
Kasschau K D, Xie Z, Allen E, Llave C, Chapman E J, Krizan K A, Carrington J C (2003). P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev Cell , 4(2): 205–217 doi: 10.1016/S1534-5807(03)00025-X
|
51 |
Kawasaki H, Taira K (2004). MicroRNA-196 inhibits HOXB8 expression in myeloid differentiation of HL60 cells. Nucleic Acids Symp Ser (Oxf) , 48(48): 211–212 doi: 10.1093/nass/48.1.211
|
52 |
Kidner C A, Martienssen R A (2003). Macro effects of microRNAs in plants. Trends Genet , 19(1): 13–16 doi: 10.1016/S0168-9525(02)00011-2
|
53 |
Krek A, Grün D, Poy M N, Wolf R, Rosenberg L, Epstein E J, MacMenamin P, da Piedade I, Gunsalus K C, Stoffel M, Rajewsky N (2005). Combinatorial microRNA target predictions. Nat Genet , 37(5): 495–500 doi: 10.1038/ng1536
|
54 |
Kren B T, Wong P Y, Sarver A, Zhang X, Zeng Y, Steer C J (2009). MicroRNAs identified in highly purified liver-derived mitochondria may play a role in apoptosis. RNA Biol , 6(1): 65–72 doi: 10.4161/rna.6.1.7534
|
55 |
Kurihara Y, Takashi Y, Watanabe Y (2006). The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA , 12(2): 206–212
|
56 |
Kurihara Y, Watanabe Y (2004). Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA , 101(34): 12753–12758 doi: 10.1073/pnas.0403115101
|
57 |
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001). Identification of novel genes coding for small expressed RNAs. Science , 294(5543): 853–858 doi: 10.1126/science.1064921
|
58 |
Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T (2003). New microRNAs from mouse and human. RNA , 9(2): 175–179
|
59 |
Lall S, Grün D, Krek A, Chen K, Wang Y L, Dewey C N, Sood P, Colombo T, Bray N, Macmenamin P, Kao H L, Gunsalus K C, Pachter L, Piano F, Rajewsky N (2006). A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol , 16(5): 460–471 doi: 10.1016/j.cub.2006.01.050
|
60 |
Lau N C, Lim L P, Weinstein E G, Bartel D P (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science , 294(5543): 858–862 doi: 10.1126/science.1065062
|
61 |
Laufs P, Peaucelle A, Morin H, Traas J (2004). MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development , 131(17): 4311–4322 doi: 10.1242/dev.01320
|
62 |
Lee C T, Risom T, Strauss W M (2007). Evolutionary conservation of microRNA regulatory circuits: an examination of microRNA gene complexity and conserved microRNA-target interactions through metazoan phylogeny. DNA Cell Biol , 26(4): 209–218 doi: 10.1089/dna.2006.0545
|
63 |
Lee R C, Ambros V (2001). An extensive class of small RNAs in Caenorhabditis elegans. Science , 294(5543): 862–864 doi: 10.1126/science.1065329
|
64 |
Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, R?dmark O, Kim S, Kim V N (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature , 425(6956): 415–419
|
65 |
Lee Y, Kim M, Han J, Yeom K H, Lee S, Baek S H, Kim V N (2004). MicroRNA genes are transcribed by RNA polymerase II. EMBO J , 23(20): 4051–4060 doi: 10.1038/sj.emboj.7600385
|
66 |
Lewis B P, Burge C B, Bartel D P (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell , 120(1): 15–20
|
67 |
Lewis B P, Shih I H, Jones-Rhoades M W, Bartel D P, Burge C B (2003). Prediction of mammalian microRNA targets. Cell , 115(7): 787–798
|
68 |
Li A, Mao L (2007). Evolution of plant microRNA gene families. Cell Res , 17(3): 212–218
|
69 |
Lim L P, Lau N C, Garrett-Engele P, Grimson A, Schelter J M, Castle J, Bartel D P, Linsley P S, Johnson J M (2005). Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature , 433(7027): 769–773 doi: 10.1038/nature03315
|
70 |
Lim L P, Lau N C, Weinstein E G, Abdelhakim A, Yekta S, Rhoades M W, Burge C B, Bartel D P (2003). The microRNAs of Caenorhabditis elegans. Genes Dev , 17(8): 991–1008 doi: 10.1101/gad.1074403
|
71 |
Liu B, Li P C, Li X, Liu C Y, Cao S Y, Chu C C, Cao X F (2005). Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol , 139(1): 296–305 doi: 10.1104/pp.105.063420
|
72 |
Llave C, Kasschau K D, Rector M A, Carrington J C (2002). Endogenous and silencing-associated small RNAs in plants. Plant Cell , 14(7): 1605–1619 doi: 10.1105/tpc.003210
|
73 |
Llave C, Xie Z, Kasschau K D, Carrington J C (2002). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science , 297(5589): 2053–2056 doi: 10.1126/science.1076311
|
74 |
Lu C, Fedoroff N V (2000). A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell , 12(12): 2351–2366
|
75 |
Lu C, Tej S S, Luo S, Haudenschild C D, Meyers B C, Green P J (2005). Elucidation of the small RNA component of the transcriptome. Science , 309(5740): 1567–1569 doi: 10.1126/science.1114112
|
76 |
Lund E, Güttinger S, Calado A, Dahlberg J E, Kutay U (2004). Nuclear export of microRNA precursors. Science , 303(5654): 95–98 doi: 10.1126/science.1090599
|
77 |
Lynn K, Fernandez A, Aida M, Sedbrook J, Tasaka M, Masson P, Barton M K (1999). The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development , 126(3): 469–481
|
78 |
Mallory A C, Bartel D P, Bartel B (2005). MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell , 17(5): 1360–1375 doi: 10.1105/tpc.105.031716
|
79 |
Mazière P, Enright A J (2007). Prediction of microRNA targets. Drug Discov Today , 12(11-12): 452–458 doi: 10.1016/j.drudis.2007.04.002
|
80 |
McHale N A, Koning R E (2004). MicroRNA-directed cleavage of Nicotiana sylvestris PHAVOLUTA mRNA regulates the vascular cambium and structure of apical meristems. Plant Cell , 16(7): 1730–1740 doi: 10.1105/tpc.021816
|
81 |
Millar A A, Gubler F (2005). The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell , 17(3): 705–721 doi: 10.1105/tpc.104.027920
|
82 |
Misson J, Raghothama K G, Jain A, Jouhet J, Block M A, Bligny R, Ortet P, Creff A, Somerville S, Rolland N, Doumas P, Nacry P, Herrerra-Estrella L, Nussaume L, Thibaud M C (2005). A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc Natl Acad Sci USA , 102(33): 11934–11939 doi: 10.1073/pnas.0505266102
|
83 |
Mittler R (2002). Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci , 7(9): 405–410 doi: 10.1016/S1360-1385(02)02312-9
|
84 |
Molnár A, Schwach F, Studholme D J, Thuenemann E C, Baulcombe D C (2007). miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature , 447(7148): 1126–1129 doi: 10.1038/nature05903
|
85 |
Morel J B, Godon C, Mourrain P, Béclin C, Boutet S, Feuerbach F, Proux F, Vaucheret H (2002). Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell , 14(3): 629–639 doi: 10.1105/tpc.010358
|
86 |
Mourrain P, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel J B, Jouette D, Lacombe A M, Nikic S, Picault N, Rémoué K, Sanial M, Vo T A, Vaucheret H (2000).Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell , 101(5): 533–542
|
87 |
Moussian B, Schoof H, Haecker A, Jürgens G, Laux T (1998). Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J , 17(6): 1799–1809 doi: 10.1093/emboj/17.6.1799
|
88 |
Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher R L, Moulton V, Dalmay T (2008). Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res , 18(10): 1602–1609 doi: 10.1101/gr.080127.108
|
89 |
Palatnik J F, Allen E, Wu X, Schommer C, Schwab R, Carrington J C, Weigel D (2003). Control of leaf morphogenesis by microRNAs. Nature , 425(6955): 257–263 doi: 10.1038/nature01958
|
90 |
Park W, Li J, Song R, Messing J, Chen X (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol , 12(17): 1484–1495 doi: 10.1016/S0960-9822(02)01017-5
|
92 |
Pasquinelli A E, Reinhart B J, Slack F, Martindale M Q, Kuroda M I, Maller B, Hayward D C, Ball E E, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature , 408(6808): 86–89 doi: 10.1038/35040556
|
93 |
Peragine A, Yoshikawa M, Wu G, Albrecht H L, Poethig R S (2004). SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev , 18(19): 2368–2379 doi: 10.1101/gad.1231804
|
94 |
Poirier Y, Bucher M (2002). Phosphate transport and homeostasis in Arabidopsis. In: Somerville C R, Meyerowitz E M, eds. The Arabidopsis Book . Rockville, MD: American Society of Plant Biologists
|
95 |
Poy M N, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald P E, Pfeffer S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M (2004). A pancreatic islet-specific microRNA regulates insulin secretion. Nature , 432(7014): 226–230 doi: 10.1038/nature03076
|
96 |
Raghothama K G (1999). Phosphate acquisition. Annu Rev Plant Physiol Plant Mol Biol , 50(1): 665–693 doi: 10.1146/annurev.arplant.50.1.665
|
97 |
Rajagopalan R, Vaucheret H, Trejo J, Bartel D P (2006). A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev , 20(24): 3407–3425 doi: 10.1101/gad.1476406
|
98 |
Reinhart B J, Weinstein E G, Rhoades M W, Bartel B, Bartel D P (2002). MicroRNAs in plants. Genes Dev , 16(13): 1616–1626 doi: 10.1101/gad.1004402
|
99 |
Rhoades M W, Reinhart B J, Lim L P, Burge C B, Bartel B, Bartel D P (2002). Prediction of plant microRNA targets. Cell , 110(4): 513–520
|
100 |
Rodriguez A, Griffiths-Jones S, Ashurst J L, Bradley A (2004). Identification of mammalian microRNA host genes and transcription units. Genome Res , 14(10A): 1902–1910 doi: 10.1101/gr.2722704
|
101 |
Sabatini S, Beis D, Wolkenfelt H, Murfett J, Guilfoyle T, Malamy J, Benfey P, Leyser O, Bechtold N, Weisbeek P, Scheres B (1999). An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root. Cell , 99(5): 463–472
|
102 |
Saunders M A, Liang H, Li W H (2007). Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci USA , 104(9): 3300–3305 doi: 10.1073/pnas.0611347104
|
103 |
Schauer S E, Jacobsen S E, Meinke D W, Ray A (2002). DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci , 7(11): 487–491 doi: 10.1016/S1360-1385(02)02355-5
|
104 |
Schwab R, Palatnik J F, Riester M, Schommer C, Schmid M, Weigel D (2005). Specific effects of microRNAs on the plant transcriptome. Dev Cell , 8(4): 517–527 doi: 10.1016/j.devcel.2005.01.018
|
105 |
Sunkar R, Girke T, Jain P K, Zhu J K (2005). Cloning and characterization of microRNAs from rice. Plant Cell , 17(5): 1397–1411 doi: 10.1105/tpc.105.031682
|
106 |
Sunkar R, Kapoor A, Zhu J K (2006). Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell , 18(8): 2051–2065 doi: 10.1105/tpc.106.041673
|
107 |
Sunkar R, Zhu J K (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell , 16(8): 2001–2019 doi: 10.1105/tpc.104.022830
|
108 |
Tan Y, Zhang B, Wu T, Skogerbθ G, Zhu X, Guo X, He S, Chen R (2009). Transcriptional inhibition of Hoxd4 expression by miRNA-10a in human breast cancer cells. BMC Mol Biol , 10(1): 12–17 doi: 10.1186/1471-2199-10-12
|
109 |
Tanzer A, Stadler P F (2004). Molecular evolution of a microRNA cluster. J Mol Biol , 339(2): 327–335 doi: 10.1016/j.jmb.2004.03.065
|
110 |
Tijsterman M, Ketting R F, Plasterk R H (2002). The genetics of RNA silencing. Annu Rev Genet , 36(1): 489–519 doi: 10.1146/annurev.genet.36.043002.091619
|
111 |
Vaucheret H, Vazquez F, Crété P, Bartel D P (2004). The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev , 18(10): 1187–1197 doi: 10.1101/gad.1201404
|
112 |
Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory A C, Hilbert J L, Bartel D P, Crété P (2004). Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell , 16(1): 69–79 doi: 10.1016/j.molcel.2004.09.028
|
114 |
Voinnet O, Pinto Y M, Baulcombe D C (1999). Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci USA , 96(24): 14147–14152 doi: 10.1073/pnas.96.24.14147
|
115 |
Volpe T A, Kidner C, Hall I M, Teng G, Grewal S I, Martienssen R A (2002). Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science , 297(5588): 1833–1837 doi: 10.1126/science.1074973
|
116 |
Wang J W, Wang L J, Mao Y B, Cai W J, Xue H W, Chen X Y (2005). Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell , 17(8): 2204–2216 doi: 10.1105/tpc.105.033076
|
117 |
Wang X J, Reyes J L, Chua N H, Gaasterland T (2004). Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol , 5(9): R65 doi: 10.1186/gb-2004-5-9-r65
|
118 |
Wasaki J, Yonetani R, Kurodas S, Shinano T, Yazaki J, (2003). Transcriptomic analysis of metabolic changes by phosphorus stress in rice plant roots. Plant Cell Environ , 26(9): 1515–1523 doi: 10.1046/j.1365-3040.2003.01074.x
|
119 |
Waterhouse P M, Graham M W, Wang M B (1998). Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA , 95(23): 13959–13964 doi: 10.1073/pnas.95.23.13959
|
120 |
Weber M J (2005). New human and mouse microRNA genes found by homology search. FEBS J , 272(1): 59–73 doi: 10.1111/j.1432-1033.2004.04389.x
|
121 |
Wilfred B R, Wang W X, Nelson P T (2007). Energizing miRNA research: a review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways. Mol Genet Metab , 91(3): 209–217 doi: 10.1016/j.ymgme.2007.03.011
|
122 |
Williams A E (2008). Functional aspects of animal microRNAs. Cell Mol Life Sci , 65(4): 545–562 doi: 10.1007/s00018-007-7355-9
|
123 |
Williams L, Grigg S P, Xie M, Christensen S, Fletcher J C (2005). Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development , 132(16): 3657–3668 doi: 10.1242/dev.01942
|
124 |
Wu F, Yu L, Cao W G, Mao Y F, Liu Z Y, He Y (2007). The N-terminal double-stranded RNA binding domains of Arabidopsis HYPONASTIC LEAVES1 are sufficient for pre-microRNA processing. Plant Cell , 19(3): 914–925 doi: 10.1105/tpc.106.048637
|
125 |
Wu P, Ma L, Hou X, Wang M, Wu Y, Liu F, Deng X W (2003). Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol , 132(3): 1260–1271 doi: 10.1104/pp.103.021022
|
126 |
Xie Z, Kasschau K D, Carrington J C (2003). Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol , 13(9): 784–789 doi: 10.1016/S0960-9822(03)00281-1
|
127 |
Yi R, Qin Y, Macara I G, Cullen B R (2003). Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev , 17(24): 3011–3016 doi: 10.1101/gad.1158803
|
128 |
Zhou G K, Kubo M, Zhong R, Demura T, Ye Z H (2007). Overexpression of miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis. Plant Cell Physiol , 48(3): 391–404 doi: 10.1093/pcp/pcm008
|
129 |
Zhou X, Ruan J, Wang G, Zhang W (2007). Characterization and identification of microRNA core promoters in four model species. PLOS Comput Biol , 3(3): e37 doi: 10.1371/journal.pcbi.0030037
|
130 |
Zilberman D, Cao X, Jacobsen S E (2003). ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science , 299(5607): 716–719 doi: 10.1126/science.1079695
|
131 |
Zilberman D, Cao X, Johansen L K, Xie Z, Carrington J C, Jacobsen S E (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol , 14(13): 1214–1220 doi: 10.1016/j.cub.2004.06.055
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