Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants. Cell 121: 207–221
Aravind L, Walker DR, Koonin E V. (1999) Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res 27: 1223–1242
Auyeung VC, Ulitsky I, McGeary SE, Bartel DP (2013) Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing. Cell 152: 844–858
Baranauskė S, Mickutė M, Plotnikova A, Finke A, Venclovas Č, Klimašauskas S, Vilkaitis G (2015) Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Res 43: 2802–2812
Baulcombe D (2004) RNA silencing in plants. Nat 2004 4317006 431: 356–363
Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs.
Bofill-De Ros X, Kasprzak WK, Bhandari Y, Fan L, Cavanaugh Q, Jiang M, Dai L, Yang A, Shao TJ, Shapiro BA, et al (2019) Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires. Cell Rep 26: 447
Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Banning C (1998) AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J 17: 170–180
Bologna NG, Iselin R, Abriata LA, Sarazin A, Pumplin N, Jay F, Grentzinger T, Dal Peraro M, Voinnet O (2018) Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway. Mol Cell 69: 709-719.e5
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
Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik JF (2013) Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Res 23: 1675
Bouché N, Lauressergues D, Gasciolli V, Vaucheret H (2006) An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J 25: 3347–56
Byrd AK, Raney KD (2012) Superfamily 2 helicases. Front Biosci (Landmark Ed 17: 2070
Carmell MA, Hannon GJ (2004) RNase III enzymes and the initiation of gene silencing. Nat Struct Mol Biol 2004 113 11: 214–218
Chan SWL, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE (2004) RNA Silencing Genes Control de Novo DNA Methylation. Science (80- ) 303: 1336
Chanfreau G, Elela SA, Ares M, Guthrie C (1997) Alternative 3′-end processing of U5 snRNA by RNase III. Genes Dev 11: 2741–2751
Chanfreau G, Rotondo G, Legrain P, Jacquier A (1998) Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO J 17: 3726–3737
Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436: 740–744
Cho SK, Chaabane S Ben, Shah P, Poulsen CP, Yang SW (2014) COP1 E3 ligase protects HYL1 to retain microRNA biogenesis. Nat Commun 5: 5867
Chomczynski P, Sacchi N (2006) The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on. Nat Protoc 2006 12 1: 581–585
Chorostecki U, Moro B, Rojas AML, Debernardi JM, Schapire AL, Notredame C, Palatnik JF (2017) Evolutionary footprints reveal insights into plant microRNA biogenesis. Plant Cell 29: 1248–1261
Clarke JH, Tack D, Findlay K, Van Montagu M, Van Lijsebettens M (1999) The SERRATE locus controls the formation of the early juvenile leaves and phase length in Arabidopsis. Plant J 20: 493–501
Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium mediated transformation of Arabidopsis thaliana. Plant J 735–743
Cordin O, Banroques J, Tanner NK, Linder P (2006) The DEAD-box protein family of RNA helicases. Gene 367: 17–37
Deng Y, Humbert S, Liu JX, Srivastava R, Rothstein SJ, Howell SH (2011) Heat induces the splicing by IRE1 of a mRNA encoding a transcription factor involved in the unfolded protein response in Arabidopsis. Proc Natl Acad Sci U S A 108: 7247–7252
Dlakić M (2006) DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold. Bioinformatics 22: 2711–2714
Dolata J, Taube M, Bajczyk M, Jarmolowski A, Szweykowska-Kulinska Z, Bielewicz D (2018) Regulation of plant microprocessor function in shaping microrna landscape. Front Plant Sci 9: 753
Dong Z, Han M-H, Fedoroff N (2008) The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci 105: 9970– 9975
Eamens AL, Smith NA, Curtin SJ, Wang M-B, Waterhouse PM (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 15: 2219–35
Elela SA, Ares M (1998) Depletion of yeast RNase III blocks correct U2 3’ end formation and results in polyadenylated but functional U2 snRNA. EMBO J 17: 3738
Elela SA, Igel H, Ares M (1996) RNase III Cleaves Eukaryotic Preribosomal RNA at a U3 snoRNP-Dependent Site. Cell 85: 115–124
Engelsberger WR, Schulze WX (2012) Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings. Plant J 69: 978–995
Fang W, Bartel DP (2015) The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes. Mol Cell 60: 131–145
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
Fang Y, Spector DL (2007) Identification of Nuclear Dicing Bodies Containing Proteins for MicroRNA Biogenesis in Living Arabidopsis Plants. Curr Biol 17: 818–823
Filippov V, Solovyev V, Filippova M, Gill SS (2000) A novel type of RNase III family proteins in eukaryotes. Gene 245: 213–221
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nat 1998 3916669 391: 806–811
Fujioka Y, Utsumi M, Ohba Y, Watanabe Y Location of a Possible miRNA Processing Site in SmD3/SmB Nuclear Bodies in Arabidopsis. doi: 10.1093/pcp/pcm099
Fukudome A, Fukuhara T (2017) Plant dicer-like proteins: double-stranded RNA-cleaving enzymes for small RNA biogenesis. J Plant Res 130: 33–44
Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD (2012) Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell 151: 533–546
Gleghorn ML, Maquat LE (2014) ‘Black sheep’ that don’t leave the double-stranded RNA- binding domain fold. Trends Biochem Sci 39: 328–340
Golden TA, Schauer SE, Lang JD, Pien S, Mushegian AR, Grossniklaus U, Meinke DW, Ray A (2002) Short Integuments1/suspensor1/carpel Factory, a Dicer Homolog, Is a Maternal Effect Gene Required for Embryo Development in Arabidopsis. Plant Physiol 130: 808–822
Grigg SP, Canales C, Hay A, Tsiantis M (2005) SERRATE coordinates shoot meristem function and leaf axial patterning in Arabidopsis. Nature 437: 1022–1026
Groot EP, Meicenheimer RD (2014) Comparison of Leaf Plastochron Index and Allometric Analyses of Tooth Development in Arabidopsis thaliana. J Plant Growth Regul 2000 191 19: 77–89
Haase AD, Jaskiewicz L, Zhang H, Lainé S, Sack R, Gatignol A, Filipowicz W (2005) TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 6: 961–967
Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN (2006) Molecular Basis for the Recognition of Primary microRNAs by the Drosha- DGCR8 Complex. Cell 125: 887–901
Han MH, Goud S, Song L, Fedoroff N (2004) The Arabidopsis double-stranded RNA- binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci U S A 101: 1093–1098
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: 173–188
Ho T, Rusholme Pilcher RL, Edwards M Lou, Cooper I, Dalmay T, Wang H (2008) Evidence for GC preference by monocot Dicer-like proteins. Biochem Biophys Res Commun 368: 433–437
Iwata Y, Ashida M, Hasegawa C, Tabara K, Mishiba KI, Koizumi N (2017) Activation of the Arabidopsis membrane-bound transcription factor bZIP28 is mediated by site-2 protease, but not site-1 protease. Plant J 91: 408–415
Iwata Y, Fedoroff N V., Koizumi N (2008) Arabidopsis bZIP60 Is a Proteolysis-Activated Transcription Factor Involved in the Endoplasmic Reticulum Stress Response. Plant Cell 20: 3107–3121
Iwata Y, Koizumi N (2012) Plant transducers of the endoplasmic reticulum unfolded protein response. Trends Plant Sci 17: 720–727
Iwata Y, Sakiyama M, Lee MH, Koizumi N (2010) Transcriptomic response of Arabidopsis thaliana to tunicamycin-induced endoplasmic reticulum stress. Plant Biotechnol 27: 161– 171
Iwata Y, Takahashi M, Fedoroff N V., Hamdan SM (2013a) Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing. Nucleic Acids Res 41: 9129–9140
Iwata Y, Takahashi M, Fedoroff N V., Hamdan SM (2013b) Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing. Nucleic Acids Res 41: 9129–9140
J M, K T, A M, J S, M S (2017) Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors. Biomed Res Int. doi: 10.1155/2017/6783010
Jacobsen SE, Running MP, Meyerowitz EM (1999) Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development 126: 5231–5243
Jankowsky E, Fairman ME (2007) RNA helicases — one fold for many functions. Curr Opin Struct Biol 17: 316–324
Jin W, Wang J, Liu CP, Wang HW, Xu RM (2020) Structural Basis for pri-miRNA Recognition by Drosha. Mol Cell 78: 423-433.e5
Johanson TM, Lew AM, Chong MMW (2013) MicroRNA-independent roles of the RNase III enzymes Drosha and Dicer. Open Biol 3: 130144
Kasschau KD, Xie Z, Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC (2003) P1/HC-Pro, a Viral Suppressor of RNA Silencing, Interferes with Arabidopsis Development and miRNA Function. Dev Cell 4: 205–217
Kidwell MA, Chan JM, Doudna JA (2014) Evolutionarily Conserved Roles of the Dicer Helicase Domain in Regulating RNA Interference Processing. J Biol Chem 289: 28352– 28362
Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 2009 102 10: 126–139
Kim W, Kim H-E, Jun AR, Jung MG, Jin S, Lee J-H, Ahn JH (2016) Structural determinants of miR156a precursor processing in temperature-responsive flowering in Arabidopsis. J Exp Bot 67: 4659–4670
Koes RE, Spelt CE, van den Elzen PJM, Mol JNM (1989) Cloning and molecular characterization of the chalcone synthase multigene family of Petunia hybrida. Gene 81: 245–257
Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) MiRBase: From microRNA sequences to function. Nucleic Acids Res 47: D155–D162
Van Der Krol AR, Mur LA, Beld M, Mol JNM, Stuitje AR (1990) Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2: 291
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: 206–212
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
Kurzynska-Kokorniak A, Pokornowska M, Koralewska N, Hoffmann W, Bienkowska- Szewczyk K, Figlerowicz M (2016) Revealing a new activity of the human Dicer DUF283 domain in vitro. Sci Reports 2016 61 6: 1–13
Kwon SC, Baek SC, Choi YG, Yang J, Lee Y suk, Woo JS, Kim VN (2019) Molecular Basis for the Single-Nucleotide Precision of Primary microRNA Processing. Mol Cell 73: 505-518.e5
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science (80- ) 294: 853–858
Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science (80- ) 294: 858–862
Lau P-W, Guiley KZ, De N, Potter CS, Carragher B, MacRae IJ (2012) The molecular architecture of human Dicer. Nat Struct Mol Biol 19: 436–440
Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Ratsch G, Weigel D (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
Lee HY, Zhou K, Smith AM, Noland CL, Doudna JA (2013) Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing. Nucleic Acids Res 41: 6568–6576
Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science (80- ) 294: 862–864
Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843–54
Lee WC, Lu SH, Lu MH, Yang CJ, Wu SH, Chen HM (2015) Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants. RNA Biol 12: 1054–1066
Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Rå Dmark O, Kim S, et al(2003) The nuclear RNase III Drosha initiates microRNA processing.
Lestini R, Delpech F, Myllykallio H (2015) DNA replication restart and cellular dynamics of Hef helicase/nuclease protein in Haloferax volcanii. Biochimie 118: 254–263
Li S, Nguyen TD, Nguyen TL, Nguyen TA (2020) Mismatched and wobble base pairs govern primary microRNA processing by human Microprocessor. Nat Commun 2020 111 11: 1–17
Liu C, Axtell MJ, Fedoroff N V. (2012) The Helicase and RNaseIIIa Domains of Arabidopsis Dicer-Like1 Modulate Catalytic Parameters during MicroRNA Biogenesis. Plant Physiol 159: 748–758
Liu C, Xin Y, Xu L, Cai Z, Xue Y, Liu Y, Xie D, Liu Y, Qi Y (2018a) Arabidopsis ARGONAUTE 1 Binds Chromatin to Promote Gene Transcription in Response to Hormones and Stresses. Dev Cell 44: 348-361.e7
Liu F, Putnam A, Jankowsky E (2008) ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proc Natl Acad Sci 105: 20209–20214
Liu Q, Rand TA, Kalidas S, Du F, Kim H-E, Smith DP, Wang X (2003) R2D2, a Bridge Between the Initiation and Effector Steps of the Drosophila RNAi Pathway. Science (80- ) 301: 1921–1925
Liu Q, Yan Q, Liu Y, Hong F, Sun Z, Shi L, Huang Y, Fang Y (2013a) Complementation of Hyponastic Leaves 1 by Double-Strand RNA-Binding Domains of Dicer-Like 1 in Nuclear Dicing Bodies 1 [ W ] [ OPEN ].
Liu Q, Yan Q, Liu Y, Hong F, Sun Z, Shi L, Huang Y, Fang Y (2013b) Complementation of Hyponastic Leaves1 by Double-Strand RNA-Binding Domains of Dicer-Like1 in Nuclear Dicing Bodies. Plant Physiol 163: 108–117
Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW (2018b) Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Cell 173: 1191-1203.e12
Loffer A, Singh J, Fukudome A, Mishra V, Wang F, Pikaard CS (2022) A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation. Elife. doi: 10.7554/ELIFE.73260
Lu C, Fedoroff N (2000) A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell 12: 2351–2366
Ma E, MacRae IJ, Kirsch JF, Doudna JA (2008) Autoinhibition of Human Dicer by Its Internal Helicase Domain. J Mol Biol 380: 237–243
Ma JB, Ye K, Patel DJ (2004) Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nat 2004 4296989 429: 318–322
Ma Z, Castillo-González C, Wang Z, Sun D, Hu X, Shen X, Potok ME, Zhang X (2018) Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression. Dev Cell 45: 769-784.e6
MacRae IJ, Zhou K, Doudna JA (2007) Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol 14: 934–940
MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA (2006) Structural Basis for Double-Stranded RNA Processing by Dicer. Science (80- ) 311: 195–198
Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J 23: 3356–3364
Manavella PA, Hagmann J, Ott F, Laubinger S, Franz M, Macek B, Weigel D (2012) Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1. Cell 151: 859–870
Mateos JL, Bologna NG, Chorostecki U, Palatnik JF (2010) Identification of MicroRNA Processing Determinants by Random Mutagenesis of Arabidopsis MIR172a Precursor. Curr Biol 20: 49–54
Meyers BC, Axtell MJ (2019) MicroRNAs in Plants: Key Findings from the Early Years. Plant Cell 31: 1206
Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, et al (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5’ terminal nucleotide. Cell 133: 116–27
Mishiba KI, Nagashima Y, Suzukia E, Hayashi N, Ogata Y, Shimada Y, Koizumi N(2013) Defects in IRE1 enhance cell death and fail to degrade mRNAs encoding secretory pathway proteins in the Arabidopsis unfolded protein response. Proc Natl Acad Sci U S A 110: 5713–5718
Mlotshwa S, Pruss GJ, Peragine A, Endres MW, Li J, Chen X, Poethig RS, Bowman LH, Vance V (2008) DICER-LIKE2 Plays a Primary Role in Transitive Silencing of Transgenes in Arabidopsis. PLoS One 3: e1755
Moro B, Chorostecki U, Arikit S, Suarez IP, Höbartner C, Rasia RM, Meyers BC, Palatnik JF (2018) Efficiency and precision of microRNA biogenesis modes in plants. Nucleic Acids Res 46: 10709–10723
Mukherjee K, Campos H, Kolaczkowski B (2013) Evolution of animal and plant dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants. Mol Biol Evol 30: 627–641
Myong S, Cui S, Cornish P V., Kirchhofer A, Gack MU, Jung JU, Hopfner KP, Ha T (2009) Cytosolic viral sensor RIG-I is a 5′-triphosphate dependent translocase on double stranded RNA. Science 323: 1070
Nagano H, Fukudome A, Hiraguri A, Moriyama H, Fukuhara T (2014) Distinct substrate specificities of Arabidopsis DCL3 and DCL4. Nucleic Acids Res 42: 1845–1856
Nagashima Y, Mishiba KI, Suzuki E, Shimada Y, Iwata Y, Koizumi N (2011) Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor. Sci Reports 2011 11 1: 1–10
Napoli C, Lemieux C, Jorgensen R (1990) Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. Plant Cell 2: 279
Narjala A, Nair A, Tirumalai V, Hari Sundar GV, Shivaprasad P V (2020) A conserved sequence signature is essential for robust plant miRNA biogenesis. Nucleic Acids Res 48: 3103–3118
Nguyen TA, Jo MH, Choi YG, Park J, Kwon SC, Hohng S, Kim VN, Woo JS (2015) Functional Anatomy of the Human Microprocessor. Cell 161: 1374–1387
De Paoli E, Dorantes-Acosta A, Jixian Z, Accerbi M, Jeong DH, Sunhee P, Meyers BC, Jorgensen RA, Green PJ (2009) Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA 15: 1965–1970
Park J-E, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN (2011) Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature 475: 201–205
Partin AC, Zhang K, Jeong BC, Herrell E, Li S, Chiu W, Nam Y (2020) Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Mol Cell 78: 411-422.e4
Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, et al (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nat 2000 4086808 408: 86–89
Prigge MJ (2001) The Arabidopsis SERRATE Gene Encodes a Zinc-Finger Protein Required for Normal Shoot Development. PLANT CELL ONLINE 13: 1263–1280
Prigge MJ, Ry Wagner D (2001) The Arabidopsis SERRATE Gene Encodes a Zinc-Finger Protein Required for Normal Shoot Development. Plant Cell 13: 1263
Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA (2010) Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction. RNA 16: 474–481
Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16: 1616–1626
Van Rij RP, Saleh MC, Berry B, Foo C, Houk A, Antoniewski C, Andino R (2006) The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes Dev 20: 2985
Rojas AML, Drusin SI, Chorostecki U, Mateos JL, Moro B, Bologna NG, Bresso EG, Schapire A, Rasia RM, Moreno DM, et al (2020) Identification of key sequence features required for microRNA biogenesis in plants. Nat Commun 2020 111 11: 1–11
Ron D, Walter P (2007) Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol 2007 87 8: 519–529
Saito K, Ishizuka A, Siomi H, Siomi MC (2005) Processing of Pre-microRNAs by the Dicer-1–Loquacious Complex in Drosophila Cells. PLOS Biol 3: e235
Schalk C, Cognat V, Graindorge S, Vincent T, Voinnet O, Molinier J (2017) Small RNA- mediated repair of UV-induced DNA lesions by the DNA damage-binding protein 2 and argonaute 1. Proc Natl Acad Sci U S A 114: E2965–E2975
Schauer SE, Jacobsen SE, Meinke DW, Ray A (2002) DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci 7: 487–491
Shabalina SA, Koonin E V. (2008) Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol 23: 578–587
Singh J, Mishra V, Wang F, Huang HY, Pikaard CS (2019) Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway. Mol Cell 75: 576-589.e5
Smith MR, Willmann MR, Wu G, Berardini TZ, Moller B, Weijers D, Poethig RS (2009) Cyclophilin 40 is required for microRNA activity in Arabidopsis. Proc Natl Acad Sci 106: 5424–5429
Song L, Axtell MJ, Fedoroff N V. (2010) RNA Secondary Structural Determinants of miRNA Precursor Processing in Arabidopsis. Curr Biol 20: 37–41
T H, H W, D P, T D (2007) Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins. FEBS Lett 581: 3267–3272
Tian Y, Simanshu DK, Ma J-B, Park J-E, Heo I, Kim VN, Patel DJ (2014) A phosphate- binding pocket within the platform-PAZ-connector helix cassette of human Dicer. Mol Cell 53: 606–16
Tsutsumi A, Kawamata T, Izumi N, Seitz H, Tomari Y (2011) Recognition of the pre- miRNA structure by Drosophila Dicer-1. Nat Struct Mol Biol 18: 1153–1158
Tsuzuki M, Nishihama R, Ishizaki K, Kurihara Y, Matsui M, Bowman JL, Kohchi T, Hamada T, Watanabe Y (2016) Profiling and Characterization of Small RNAs in the Liverwort, Marchantia polymorpha , Belonging to the First Diverged Land Plants. Plant Cell Physiol 57: 359–372
Tworak A, Urbanowicz A, Podkowinski J, Kurzynska-Kokorniak A, Koralewska N, Figlerowicz M (2016) Six Medicago truncatula Dicer-like protein genes are expressed in plant cells and upregulated in nodules. Plant Cell Rep 35: 1043
Upton J-P, Wang L, Han D, Wang ES, Huskey NE, Lim L, Truitt M, McManus MT, Ruggero D, Goga A, et al (2012) IRE1 Cleaves Select microRNAs During ER Stress to Derepress Translation of Proapoptotic Caspase-2. Science (80- ) 338: 818–822
Valli AA, Santos BACM, Hnatova S, Bassett AR, Molnar A, Chung BY, Baulcombe DC (2016) Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs. Genome Res 26: 519–529
Varkonyi-Gasic E, Hellens RP (2010) qRT-PCR of Small RNAs. Methods Mol Biol 631: 109–122
Vaucheret H (2008) Plant ARGONAUTES. Trends Plant Sci 13: 350–358
Vazquez F, Gasciolli V, Crété P, Vaucheret H (2004) The Nuclear dsRNA Binding Protein HYL1 Is Required for MicroRNA Accumulation and Plant Development, but Not Posttranscriptional Transgene Silencing. Curr Biol 14: 346–351
Voinnet O (2009) Origin, Biogenesis, and Activity of Plant MicroRNAs. Cell 136: 669–687
Walter P, Ron D (2011) The unfolded protein response: From stress pathway to homeostatic regulation. Science (80- ) 334: 1081–1086
Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Jake Harris C, Wu Z, et al (2021) Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science (80- ) 374: 1152–1157
Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y (2021) Structural basis of microRNA processing by Dicer-like 1. Nat Plants 2021 710 7: 1389–1396
Werner S, Wollmann H, Schneeberger K, Weigel D (2010) Structure Determinants for Accurate Processing of miR172a in Arabidopsis thaliana. Curr Biol 20: 42–48
Wilson RC, Doudna JA (2013) Molecular mechanisms of RNA interference. Annu Rev Biophys 42: 217
Wu F, Yu L, Cao W, Mao Y, Liu Z, Hea Y (2007) The N-Terminal Double-Stranded RNA Binding Domains of Arabidopsis HYPONASTIC LEAVES1 Are Sufficient for Pre- MicroRNA Processing. Plant Cell 19: 914
Wu MF, Tian Q, Reed JW (2006) Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133: 4211–4218
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and Functional Diversification of Small RNA Pathways in Plants. PLoS Biol 2: e104
Xie Z, Kasschau KD, Carrington JC (2003) Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol 13: 784–9
Yan KS, Yan S, Farooq A, Han A, Zeng L, Zhou MM (2003) Structure and conserved RNA binding of the PAZ domain. Nat 2003 4266965 426: 469–474
Yang L, Liu Z, Lu F, Dong A, Huang H (2006) SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J 47: 841–850
Yang SW, Chen H-Y, Yang J, Machida S, Chua N-H, Yuan YA (2010) Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure 18: 594–605
Yang X, Dong W, Ren W, Zhao Q, Wu F, He Y (2021) Cytoplasmic HYL1 modulates miRNA-mediated translational repression. Plant Cell 33: 1980–1996
Yang X, Ren W, Zhao Q, Zhang P, Wu F, He Y (2014) Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA. Nucleic Acids Res 42: 12224–12236
Yao X, Chen J, Zhou J, Yu H, Ge C, Zhang M, Gao X, Dai X, Yang Z-N, Zhao Y An Essential Role for miRNA167 in Maternal Control of Embryonic and Seed Development 1[OPEN]. doi: 10.1104/pp.19.00127
Ye X, Paroo Z, Liu Q (2007) Functional Anatomy of the Drosophila MicroRNA-generating Enzyme. J Biol Chem 282: 28373–28378
Yoneyama M, Kikuchi M, Natsukawa T, Shinobu N, Imaizumi T, Miyagishi M, Taira K, Akira S, Fujita T (2004) The RNA helicase RIG-I has an essential function in double- stranded RNA-induced innate antiviral responses. Nat Immunol 2004 57 5: 730–737
Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X (2005) Methylation as a Crucial Step in Plant microRNA Biogenesis. Science (80- ) 307: 932– 935
Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single Processing Center Models for Human Dicer and Bacterial RNase III. Cell 118: 57–68
Zhang Z, Guo X, Ge C, Ma Z, Jiang M, Li T, Koiwa H, Yang SW, Zhang X (2017) KETCH1 imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis. Proc Natl Acad Sci 114: 4011–4016
Zhu H, Zhou Y, Castillo-González C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJ, Wang XJ, et al (2013) Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nat Struct Mol Biol 20: 1106–1115
Zou J, Chang M, Nie P, Secombes CJ (2009) Origin and evolution of the RIG-I like RNA helicase gene family. BMC Evol Biol 9: 1–14
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415
木上 椋介（2020）シロイヌナズナ microRNA 関連タンパク質間の相互作用とキュウリモザイクウイルス 2b による microRNA 経路の阻害様式の解析（修士論文）
論文の公開元へ
