[1] MCKEOWN P C, SPILLANE C. Landscaping plant epigenetics [J]. Methods Molecular Biology, 2014, 1112: 1-24.
[2] HOLLIDAY R. Epigenetics A Historical Overview [J]. Epigenetics, 2006, 1(2): 76-80.
[3] BERGER S L, KOUZARIDES T, SHIEKHATTAR R, et al. An operational definition of epigenetics [J]. Genes Development, 2009, 23(7): 781-783.
[4] PECINKA A, MITTELSTEN SCHEID O. Stress-induced chromatin changes: a critical view on their heritability [J]. Plant and Cell Physiology, 2012, 53(5): 801-808.
[5] WANG J W, QI Y. Plant non-coding RNAs and epigenetics [J]. Science China Life Sciences, 2018, 61(2): 135-137.
[6] HAUSER M T, AUFSATZ W, JONAK C, et al. Transgenerational epigenetic inheritance in plants [J]. Biochimca et Biophysica Acta, 2011, 1809(8): 459-468.
[7] RAINA M, IBBA M. tRNAs as regulators of biological processes [J]. Frontiers in Genetics, 2014, 5: 171.
[8] XU X W, ZHOU X H, WANG R R, et al. Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network [J]. Scientific Reports, 2016, 6.
[9] WANG J J, MENG X W, DOBROVOLSKAYA O B, et al. Non-coding RNAs and Their Roles in Stress Response in Plants [J]. Genomics, Proteomics & Bioinformatics, 2017, 15(5): 301-312.
[10] DI C, YUAN J P, WU Y, et al. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features [J]. Plant Journal, 2014, 80(5): 848-861.
[11] SONG X W, LI Y, CAO X F, et al. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions [J]. Annual Review of Plant Biology, Vol 70, 2019, 70: 489-525.
[12] AU P C, ZHU Q H, DENNIS E S, et al. Long non-coding RNA-mediated mechanisms independent of the RNAi pathway in animals and plants [J]. RNA Biology, 2011, 8(3): 404-414.
[13] LUCERO L, FONOUNI-FARDE C, CRESPI M, et al. Long noncoding RNAs shape transcription in plants [J]. Transcription, 2020, 11(3-4): 160-171.
[14] XU C, TIAN J, MO B. siRNA-mediated DNA methylation and H3K9 dimethylation in plants [J]. Protein Cell, 2013, 4(9): 656-663.
[15] HUANG Y, LI Y. Secondary siRNAs rescue virus-infected plants [J]. Nature Plants, 2018, 4(3): 136-137.
[16] SANAN-MISHRA N, ABDUL KADER JAILANI A, MANDAL B, et al. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology [J]. Frontiers in Plant Science, 2021, 12: 610283.
[17] KHRAIWESH B, ZHU J K, ZHU J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants [J]. Biochimica et Biophysica Acta, 2012, 1819(2): 137-148.
[18] IWAKAWA H O, LAM A Y W, MINE A, et al. Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants [J]. Cell Reports, 2021, 35(13): 109300.
[19] WU L. DICER-LIKE1 processed trans-acting siRNAs mediate DNA methylation: case study of complex small RNA biogenesis and action pathways in plants [J]. Plant Signal & Behavior, 2013, 8(1): e22476.
[20] LI Y, DENG C, SHANG Q, et al. Characterization of siRNAs derived from cucumber green mottle mosaic virus in infected cucumber plants [J]. Archives of Virology, 2016, 161(2): 455-458.
[21] QIAO W, ZARZYNSKA-NOWAK A, NERVA L, et al. Accumulation of 24 nucleotide transgene-derived siRNAs is associated with crinivirus immunity in transgenic plants [J]. Molecular Plant Pathology, 2018, 19(10): 2236-2247.
[22] YANG X, ZHANG L, YANG Y, et al. miRNA Mediated Regulation and Interaction between Plants and Pathogens [J]. International Journal of Molecular Sciences, 2021, 22(6): 2913.
[23] SHAH S M S, ULLAH F. A comprehensive overview of miRNA targeting drought stress resistance in plants [J]. Brazilian Journal of Biology, 2021, 83: e242708.
[24] BOUBA I, KANG Q, LUAN Y S, et al. Predicting miRNA-lncRNA interactions and recognizing their regulatory roles in stress response of plants [J]. Mathematical Bioscience, 2019, 312: 67-76.
[25] ZHU L, OW D W, DONG Z C. Transfer RNA-derived small RNAs in plants [J]. Science China Life Science, 2018, 61(2): 155-161.
[26] GUTBROD M J, MARTIENSSEN R A. Conserved chromosomal functions of RNA interference [J]. Nature Reviews Genetics, 2020, 21(5): 311-331.
[27] CHEN C J, LI J W, FENG J T, et al. sRNAanno-a database repository of uniformly annotated small RNAs in plants [J]. Horticulture Research, 2021, 8(1): 45.
[28] GUO Z L, KUANG Z, WANG Y, et al. PmiREN: a comprehensive encyclopedia of plant miRNAs [J]. Nucleic Acids Research, 2020, 48(D1): D1114-D1121.
[29] STEPIEN A, KNOP K, DOLATA J, et al. Posttranscriptional coordination of splicing and miRNA biogenesis in plants [J]. Wiley Interdisciplinary Reviews: RNA, 2017, 8(3): e1403.
[30] CHO S K, RYU M Y, SHAH P, et al. Post-Translational Regulation of miRNA Pathway Components, AGO1 and HYL1, in Plants [J]. Molecules and Cells, 2016, 39(8): 581-586.
[31] FEI Q L, XIA R, MEYERS B C. Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks [J]. Plant Cell, 2013, 25(7): 2400-2415.
[32] SANAN-MISHRA N, JAILANI A A K, MANDAL B, et al. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology [J]. Frontiers in Plant Science, 2021, 12: 610283.
[33] ALLEN E, XIE Z X, GUSTAFSON A I, et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants (Reprinted from Cell, vol 121, pg 207-221, 2005) [J]. Cell, 2007, 131(4): 74-88.
[34] AREGGER M, BORAH B K, SEGUIN J, et al. Primary and Secondary siRNAs in Geminivirus-induced Gene Silencing [J]. PLOS Pathogens, 2012, 8(9): e1002941.
[35] CUPERUS J T, CARBONELL A, FAHLGREN N, et al. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis [J]. Nature Structural & Molecular Biology, 2010, 17(8): 997-1003.
[36] AXTELL M J. Classification and comparison of small RNAs from plants [J]. Annual Review of Plant Biology, 2013, 64: 137-159.
[37] BORGES F, MARTIENSSEN R A. The expanding world of small RNAs in plants [J]. Nature Reviews Molecular Cell Biology, 2015, 16(12): 727-741.
[38] SIMON S A, MEYERS B C. Small RNA-mediated epigenetic modifications in plants [J]. Current Opinion in Plant Biology, 2011, 14(2): 148-155.
[39] BORGES F, MARTIENSSEN R A. The expanding world of small RNAs in plants [J]. Nature Reviews Molecular Cell Biology, 2015, 16(12): 727-741.
[40] PALAUQUI J C, ELMAYAN T, DEBORNE F D, et al. Frequencies, timing, and spatial patterns of co-suppression of nitrate reductase and nitrite reductase in transgenic tobacco plants [J]. Plant Physiology, 1996, 112(4): 1447-1456.
[41] UDDIN M N, KIM J Y. Non-cell-autonomous RNA silencing spread in plants [J]. Botanical Studies, 2011, 52(2): 129-136.
[42] VOINNET O. Non-cell autonomous RNA silencing [J]. FEBS Letters, 2005, 579(26): 5858-5871.
[43] KALANTIDIS K, SCHUMACHER H T, ALEXIADIS T, et al. RNA silencing movement in plants [J]. Biology of the Cell, 2008, 100(1): 13-26.
[44] HENDERSON I R, ZHANG X, LU C, et al. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning [J]. Nature Genetics, 2006, 38(6): 721-725.
[45] GASCIOLLI V, MALLORY A C, BARTEL D P, et al. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs [J]. Current Biology, 2005, 15(16): 1494-1500.
[46] FUKUDOME A, FUKUHARA T. Plant dicer-like proteins: double-stranded RNA-cleaving enzymes for small RNA biogenesis [J]. Journal of Plant Research, 2017, 130(1): 33-44.
[47] HO T, WANG L, HUANG L, et al. Nucleotide bias of DCL and AGO in plant anti-virus gene silencing [J]. Protein&Cell, 2010, 1(9): 847-858.
[48] DALMADI A, GYULA P, BALINT J, et al. AGO-unbound cytosolic pool of mature miRNAs in plant cells reveals a novel regulatory step at AGO1 loading [J]. Nucleic Acids Research, 2019, 47(18): 9803-9817.
[49] ZHAI J X, BISCHOF S, WANG H F, et al. A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis [J]. Cell, 2015, 163(2): 445-455.
[50] MATZKE M A, MOSHER R A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity (vol 15, 394, 2014) [J]. Nature Reviews Genetics, 2014, 15(8): 394-408
[51] HUNG Y H, SLOTKIN R K. The initiation of RNA interference (RNAi) in plants [J]. Current Opinion in Plant Biology, 2021, 61: 102014.
[52] ZHANG H M, LANG Z B, ZHU J K. Dynamics and function of DNA methylation in plants [J]. Nature Reviews Molecular Cell Biology, 2018, 19(8): 489-506.
[53] SUN T, ZHOU Q, ZHOU Z, et al. SQUINT Positively Regulates Resistance to the Pathogen Botrytis cinerea via miR156-SPL9 Module in Arabidopsis [J]. Plant Cell Physiology, 2022, pcac042.
[54] ZHOU Q, SHI J, LI Z, et al. miR156/157 Targets SPLs to Regulate Flowering Transition, Plant Architecture and Flower Organ Size in Petunia [J]. Plant Cell Physiology, 2021, 62(5): 839-857.
[55] CARLSBECKER A, LEE J Y, ROBERTS C J, et al. Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate [J]. Nature, 2010, 465(7296): 316-321.
[56] NODINE M D, BARTEL D P. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis [J]. Genes & Development, 2010, 24(23): 2678-2692.
[57] MATZKE M A, MOSHER R A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity [J]. Nature Reviews Genetics, 2014, 15(6): 394-408.
[58] SLOTKIN R K, MARTIENSSEN R. Transposable elements and the epigenetic regulation of the genome [J]. Nature Reviews Genetics, 2007, 8(4): 272-285.
[59] YOSHIKAWA M, PERAGINE A, PARK M Y, et al. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis [J]. Genes & Development, 2005, 19(18): 2164-2175.
[60] AXTELL M J, JAN C, RAJAGOPALAN R, et al. A two-hit trigger for siRNA biogenesis in plants [J]. Cell, 2006, 127(3): 565-577.
[61] BOUCHE N, LAURESSERGUES D, GASCIOLLI V, et al. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs [J]. The EMBO Journal, 2006, 25(14): 3347-3456.
[62] CHEN D, MENG Y, MA X, et al. Small RNAs in angiosperms: sequence characteristics, distribution and generation [J]. Bioinformatics, 2010, 26(11): 1391-1394.
[63] GARCIA-RUIZ H, TAKEDA A, CHAPMAN E J, et al. Arabidopsis RNA-Dependent RNA Polymerases and Dicer-Like Proteins in Antiviral Defense and Small Interfering RNA Biogenesis during Turnip Mosaic Virus Infection [J]. The Plant Cell, 2010, 22(2): 481-496.
[64] GARCIA-RUIZ H, TAKEDA A, CHAPMAN E J, et al. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip mosaic virus infection (vol 22, pg 481, 2010) [J]. The Plant Cell, 2015, 27(3): 944-945.
[65] QIN C, LI B, FAN Y Y, et al. Roles of Dicer-Like Proteins 2 and 4 in Intra- and Intercellular Antiviral Silencing [J]. Plant Physiology, 2017, 174(2): 1067-1081.
[66] CREASEY K M, ZHAI J, BORGES F, et al. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis [J]. Nature, 2014, 508(7496): 411-415.
[67] ZHAI J, ZHANG H, ARIKIT S, et al. Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers [J]. Proceedings of the National Academy of Sciences, 2015, 112(10): 3146-3151.
[68] DUKOWIC-SCHULZE S, SUNDARARAJAN A, RAMARAJ T, et al. Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis [J]. Frontiers in Plant Science, 2016, 7: 762.
[69] TENG C, ZHANG H, HAMMOND R, et al. Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize [J]. Nature Communications, 2020, 11(1): 2912.
[70] DUKOWIC-SCHULZE S, SUNDARARAJAN A, RAMARAJ T, et al. Corrigendum: Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis [J]. Frontiers in Plant Science, 2020, 11: 653.
[71] CHEN H M, CHEN L T, PATEL K, et al. 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants [J]. Proceedings of the National Academy of Sciences, 2010, 107(34): 15269-15274.
[72] XIE D, CHEN M, NIU J, et al. Phase separation of SERRATE drives dicing body assembly and promotes miRNA processing in Arabidopsis [J]. Nature Cell Biology, 2021, 23(1): 32-39.
[73] WERNER S, WOLLMANN H, SCHNEEBERGER K, et al. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana [J]. Current Biology, 2010, 20(1): 42-48.
[74] SONG L, AXTELL M J, FEDOROFF N V. RNA secondary structural determinants of miRNA precursor processing in Arabidopsis [J]. Current Biology, 2010, 20(1): 37-41.
[75] MATEOS J L, BOLOGNA N G, CHOROSTECKI U, et al. Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor [J]. Current Biology, 2010, 20(1): 49-54.
[76] ZHU H, ZHOU Y, CASTILLO-GONZALEZ C, et al. Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1 [J]. Nature Structural & Molecular Biology, 2013, 20(9): 1106-1115.
[77] MENG Y, SHAO C, WANG H, et al. Uncovering DCL1-dependent small RNA loci on plant genomes: a structure-based approach [J]. J Environmental and Experimental Botany, 2014, 65(2): 395-400.
[78] DONG Z, HAN M H, FEDOROFF N. The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1 [J]. Proceedings of the National Academy of Sciences, 2008, 105(29): 9970-9975.
[79] WEI X, KE H, WEN A, et al. Structural basis of microRNA processing by Dicer-like 1 [J]. Nature Plants, 2021, 7(10): 1389-1396.
[80] MONTAVON T, KWON Y, ZIMMERMANN A, et al. Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates [J]. The Plant Journal, 2018, 95(2): 204-218.
[81] NAGANO H, FUKUDOME A, HIRAGURI A, et al. Distinct substrate specificities of Arabidopsis DCL3 and DCL4 [J]. Nucleic Acids Research, 2014, 42(3): 1845-1856.
[82] WU Y Y, HOU B H, LEE W C, et al. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation [J]. The Plant Journal, 2017, 90(6): 1064-1078.
[83] KAKIYAMA S, TABARA M, NISHIBORI Y, et al. Long DCL4-substrate dsRNAs efficiently induce RNA interference in plant cells [J]. Scientific Reports, 2019, 9(1): 6920.
[84] PARENT J S, BOUTEILLER N, ELMAYAN T, et al. Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing [J]. The Plant Journal, 2015, 81(2): 223-232.
[85] QIN H, CHEN F, HUAN X, et al. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction [J]. Rna, 2010, 16(3): 474-481.
[86] NAKAZAWA Y, HIRAGURI A, MORIYAMA H, et al. The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway [J]. Plant Molecular Biology, 2007, 63(6): 777-785.
[87] LOFFER A, SINGH J, FUKUDOME A, et al. A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation [J]. Elife, 2022, 11: e73260.
[88] WENDTE J M, PIKAARD C S. The RNAs of RNA-directed DNA methylation [J]. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms, 2017, 1860(1): 140-148.
[89] HUANG K, WU X X, FANG C L, et al. Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA [J]. Science, 2021, 374(6575): 1579-1586.
[90] BLEVINS T, PODICHETI R, MISHRA V, et al. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis [J]. Elife, 2015, 4: e09591.
[91] LI S, VANDIVIER L E, TU B, et al. Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis [J]. Genome Research, 2015, 25(2): 235-245.
[92] PIKAARD C S, HAAG J R, REAM T, et al. Roles of RNA polymerase IV in gene silencing [J]. Trends in Plant Science, 2008, 13(7): 390-397.
[93] SINGH J, MISHRA V, WANG F, et al. Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway [J]. Molecular Cell, 2019, 75(3): 576-589.
[94] ZILBERMAN D, CAO X, JACOBSEN S E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation [J]. Science, 2003, 299(5607): 716-719.
[95] MUKHERJEE K, CAMPOS H, KOLACZKOWSKI B. Evolution of Animal and Plant Dicers: Early Parallel Duplications and Recurrent Adaptation of Antiviral RNA Binding in Plants [J]. Molecular Biology and Evolution, 2013, 30(3): 627-641.
[96] WILLMANN M R, ENDRES M W, COOK R T, et al. The Functions of RNA-Dependent RNA Polymerases in Arabidopsis [J]. The Arabidopsis Book, 2011, 9: e0146.
[97] LU S, SHI R, TSAO C C, et al. RNA silencing in plants by the expression of siRNA duplexes [J]. Nucleic Acids Research, 2004, 32(21): e171.
[98] WEI L Y, GU L F, SONG X W, et al. Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice [J]. Proceedings of the National Academy of Sciences, 2014, 111(10): 3877-3882.
[99] DU Z, LEE J K, TJHEN R, et al. Structural and biochemical insights into the dicing mechanism of mouse Dicer: A conserved lysine is critical for dsRNA cleavage [J]. Proceedings of the National Academy of Sciences, 2008, 105(7): 2391-2396.
[100] PARENT J S, BOUTEILLER N, ELMAYAN T, et al. Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing [J]. The Plant Journal, 2015, 81(2): 223-232.
[101] JIA J B, JI R H, LI Z W, et al. Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats [J]. The Plant Cell, 2020, 32(12): 3662-3673.
[102] DENIZ O, FROST J M, BRANCO M R. Regulation of transposable elements by DNA modifications [J]. Nature Reviews Genetics, 2019, 20(7): 417-431.
[103] ZHANG H, LANG Z, ZHU J K. Dynamics and function of DNA methylation in plants [J]. Nature Reviews Molecular Cell Biology, 2018, 19(8): 489-506.
[104] WASSENEGGER M, HEIMES S, RIEDEL L, et al. RNA-directed de novo methylation of genomic sequences in plants [J]. Cell, 1994, 76(3): 567-576.
[105] ZHANG X, YAZAKI J, SUNDARESAN A, et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis [J]. Cell, 2006, 126(6): 1189-1201.
[106] LAW J A, JACOBSEN S E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals [J]. Nature Reviews Genetics, 2010, 11(3): 204-220.
[107] HAAG J R, REAM T S, MARASCO M, et al. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing [J]. Molecular Cell, 2012, 48(5): 811-818.
[108] WIERZBICKI A T, REAM T S, HAAG J R, et al. RNA polymerase V transcription guides ARGONAUTE4 to chromatin [J]. Nature Genetics, 2009, 41(5): 630-634.
[109] WIERZBICKI A T, HAAG J R, PIKAARD C S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes [J]. Cell, 2008, 135(4): 635-648.
[110] ZHENG Z, XING Y, HE X J, et al. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis [J]. The Plant Journal, 2010, 62(1): 92-99.
[111] AUSIN I, GREENBERG M V, SIMANSHU D K, et al. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [J]. Proceedings of the National Academy of Sciences, 2012, 109(22): 8374-8381.
[112] AUSIN I, MOCKLER T C, CHORY J, et al. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana [J]. Nature Structural & Molecular Biology, 2009, 16(12): 1325-1327.
[113] LAHMY S, BIES-ETHEVE N, LAGRANGE T. Plant-specific multisubunit RNA polymerase in gene silencing [J]. Epigenetics, 2010, 5(1): 4-8.
[114] MOSHER R A, MELNYK C W, KELLY K A, et al. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis [J]. Nature, 2009, 460(7252): 283-286.
[115] JOHNSON L M, DU J, HALE C J, et al. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation [J]. Nature, 2014, 507(7490): 124-128.
[116] JOHNSON L M, DU J, HALE C J, et al. Corrigendum: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation [J]. Nature, 2017, 543(7643): 136.
[117] HENDERSON I R, JACOBSEN S E. Epigenetic inheritance in plants [J]. Nature, 2007, 447(7143): 418-424.
[118] LISTER R, O'MALLEY R C, TONTI-FILIPPINI J, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis [J]. Cell, 2008, 133(3): 523-536.
[119] LAW J A, DU J, HALE C J, et al. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1 [J]. Nature, 2013, 498(7454): 385-389.
[120] VAN DER KROL A R, MUR L A, BELD M, et al. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression [J]. The Plant Cell, 1990, 2(4): 291-299.
[121] FIRE A, XU S, MONTGOMERY M K, et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans [J]. Nature, 1998, 391(6669): 806-811.
[122] JIN L, CHEN M, XIANG M, et al. RNAi-Based Antiviral Innate Immunity in Plants [J]. Viruses, 2022, 14(2): 432.
[123] TRUNIGER V, ARANDA M A. Recessive resistance to plant viruses [J]. Advances in Virus Research, 2009, 75: 119-159.
[124] ABEL P P, NELSON R S, DE B, et al. Delay of disease development in transgenic plants that express the tobacco mosaic virus coat protein gene [J]. Science, 1986, 232(4751): 738-743.
[125] GUO Z, LI Y, DING S W. Small RNA-based antimicrobial immunity [J]. Nature Reviews Immunology, 2019, 19(1): 31-44.
[126] SZITTYA G, BURGYAN J. RNA interference-mediated intrinsic antiviral immunity in plants [J]. Current Topics in Microbiology and Immunology, 2013, 371: 153-181.
[127] MARTIENSSEN R, MOAZED D. RNAi and heterochromatin assembly [J]. Cold Spring Harbor Perspectives in Biology, 2015, 7(8): a019323.
[128] WASSENEGGER M, KRCZAL G. Nomenclature and functions of RNA-directed RNA polymerases [J]. Trends in Plant Science, 2006, 11(3): 142-151.
[129] VAZQUEZ F, LEGRAND S, WINDELS D. The biosynthetic pathways and biological scopes of plant small RNAs [J]. Trends in Plant Science, 2010, 15(6): 337-345.
[130] DING S W. RNA-based antiviral immunity [J]. Nature Reviews Immunology, 2010, 10(9): 632-644.
[131] DUNOYER P, MELNYK C, MOLNAR A, et al. Plant mobile small RNAs [J]. Cold Spring Harbor Perspectives in Biology, 2013, 5(7): a017897.
[132] BRUMMELKAMP T R, BERNARDS R, AGAMI R. A system for stable expression of short interfering RNAs in mammalian cells [J]. Science, 2002, 296(5567): 550-553.
[133] ZUCKERMAN J E, DAVIS M E. Clinical experiences with systemically administered siRNA-based therapeutics in cancer [J]. Nature Reviews Drug Discovery, 2015, 14(12): 843-856.
[134] MATHEW V, WANG A K. Inotersen: new promise for the treatment of hereditary transthyretin amyloidosis [J]. Drug Design, Development and Therapy, 2019, 13: 1515-1525.
[135] SYED Y Y. Givosiran: A Review in Acute Hepatic Porphyria [J]. Drugs, 2021, 81(7): 841-848.
[136] FRESSIGNE L, SIMARD M J. Biogenesis of small non-coding RNAs in animals [J]. Medical Sciences, 2018, 34(2): 137-144.
[137] KIM V N, HAN J, SIOMI M C. Biogenesis of small RNAs in animals [J]. Nature Reviews Molecular Cell Biology, 2009, 10(2): 126-139.
[138] CARMELL M A, HANNON G J. RNase III enzymes and the initiation of gene silencing [J]. Nature Structural & Molecular Biology, 2004, 11(3): 214-218.
[139] HAMMOND S M. Dicing and slicing - The core machinery of the RNA interference pathway [J]. FEBS Letters, 2005, 579(26): 5822-5829.
[140] LEE Y S, NAKAHARA K, PHAM J W, et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways [J]. Cell, 2004, 117(1): 69-81.
[141] MACRAE I J, ZHOU K H, LI F, et al. Structural basis for double-stranded RNA processing by dicer [J]. Science, 2006, 311(5758): 195-198.
[142] KWON S C, NGUYEN T A, CHOI Y G, et al. Structure of Human DROSHA [J]. Cell, 2016, 164(1-2): 81-90.
[143] PARTIN A C, ZHANG K M, JEONG B C, et al. Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA [J]. Molecular Cell, 2020, 78(3): 411-422.
[144] NGUYEN T A, JO M H, CHOI Y G, et al. Functional Anatomy of the Human Microprocessor [J]. Cell, 2015, 161(6): 1374-1387.
[145] SINHA N K, IWASA J, SHEN P S, et al. Dicer uses distinct modules for recognizing dsRNA termini [J]. Science, 2018, 359(6373): 329-334.
[146] MACRAE I J, MA E, ZHOU M, et al. In vitro reconstitution of the human RISC-loading complex [J]. Proceedings of the National Academy of Sciences, 2008, 105(2): 512-517.
[147] ZHANG H D, KOLB F A, JASKIEWICZ L, et al. Single processing center models for human dicer and bacterial RNase III [J]. Cell, 2004, 118(1): 57-68.
[148] PARK J E, HEO I, TIAN Y, et al. Dicer recognizes the 5' end of RNA for efficient and accurate processing [J]. Nature, 2011, 475(7355): 201-205.
[149] SINGH J, MISHRA V, WANG F, et al. Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway [J]. Molecular Cell, 2019, 75(3): 576-589. e5.
[150] MA E, MACRAE I J, KIRSCH J F, et al. Autoinhibition of human dicer by its internal helicase domain [J]. J Mol Biol, 2008, 380(1): 237-243.
[151] MACRAE I J, ZHOU K, DOUDNA J A. Structural determinants of RNA recognition and cleavage by Dicer [J]. Nature Structural & Molecular Biology, 2007, 14(10): 934-940.
[152] PROVOST P, DISHART D, DOUCET J, et al. Ribonuclease activity and RNA binding of recombinant human Dicer [J]. The EMBO Journal, 2002, 21(21): 5864-5874.
[153] HOEHENER C, HUG I, NOWACKI M. Dicer-like Enzymes with Sequence Cleavage Preferences [J]. Cell, 2018, 173(1): 234-47 e7.
[154] MATSUDA T, CEPKO C L. Electroporation and RNA interference in the rodent retina in vivo and in vitro [J]. Proceedings of the National Academy of Sciences, 2004, 101(1): 16-22.
[155] MOCHIZUKI K, GOROVSKY M A. A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase [J]. Genes & Development, 2005, 19(1): 77-89.
[156] TIAN Y, SIMANSHU D K, MA J B, et al. A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer [J]. Molecular Cell, 2014, 53(4): 606-616.
[157] DENLI A M, TOPS B B, PLASTERK R H, et al. Processing of primary microRNAs by the Microprocessor complex [J]. Nature, 2004, 432(7014): 231-235.
[158] HAN J, LEE Y, YEOM K H, et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex [J]. Cell, 2006, 125(5): 887-901.
[159] WANG T, DENG Z, ZHANG X, et al. Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV [J]. Horticulture Research, 2018, 5: 62.
[160] GAN J, SHAW G, TROPEA J E, et al. A stepwise model for double-stranded RNA processing by ribonuclease III [J]. Molecular Microbiology, 2008, 67(1): 143-154.
[161] JIN W, WANG J, LIU C P, et al. Structural Basis for pri-miRNA Recognition by Drosha [J]. Molecular Cell, 2020, 78(3): 423-433.
[162] LIU Z M, WANG J, CHENG H, et al. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate [J]. Cell, 2018, 173(5): 1191-1203.
[163] DANIELS S M, MELENDEZ-PENA C E, SCARBOROUGH R J, et al. Characterization of the TRBP domain required for dicer interaction and function in RNA interference [J]. BMC Molecular Biology, 2009, 10: 38.
[164] WILSON R C, TAMBE A, KIDWELL M A, et al. Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis [J]. Molecular Cell, 2015, 57(3): 397-407.
[165] GAN J, TROPEA J E, AUSTIN B P, et al. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III [J]. Cell, 2006, 124(2): 355-366.
[166] MACRAE I J, ZHOU K, DOUDNA J A. Structural determinants of RNA recognition and cleavage by Dicer [J]. Nature Structural & Molecular Biology, 2007, 14(10): 934-940.
[167] LAU P W, POTTER C S, CARRAGHER B, et al. Structure of the human Dicer-TRBP complex by electron microscopy [J]. Structure, 2009, 17(10): 1326-1332.
[168] LAU P W, GUILEY K Z, DE N, et al. The molecular architecture of human Dicer [J]. Nature Structural & Molecular Biology, 2012, 19(4): 436-440.
[169] BLASZCZYK J, TROPEA J E, BUBUNENKO M, et al. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage [J]. Structure, 2001, 9(12): 1225-1236.
[170] ZAMORE P D. Thirty-three years later, a glimpse at the ribonuclease III active site [J]. Molecular Cell, 2001, 8(6): 1158-1160.
[171] SUN W, PERTZEV A, NICHOLSON A W. Catalytic mechanism of Escherichia coli ribonuclease III: kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis [J]. Nucleic Acids Research, 2005, 33(3): 807-815.
[172] AMARASINGHE A K, CALIN-JAGEMAN I, HARMOUCH A, et al. Escherichia coli ribonuclease III: affinity purification of hexahistidine-tagged enzyme and assays for substrate binding and cleavage [J]. Methods in Enzymology, 2001, 342: 143-158.
[173] CAMPBELL F E, JR., CASSANO A G, ANDERSON V E, et al. Pre-steady-state and stopped-flow fluorescence analysis of Escherichia coli ribonuclease III: insights into mechanism and conformational changes associated with binding and catalysis [J]. Journal of Molecular Biology, 2002, 317(1): 21-40.
[174] LI H L, CHELLADURAI B S, ZHANG K, et al. Ribonuclease III cleavage of a bacteriophage T7 processing signal. Divalent cation specificity, and specific anion effects [J]. Nucleic Acids Research, 1993, 21(8): 1919-1925.
[175] MA J B, YE K, PATEL D J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain [J]. Nature, 2004, 429(6989): 318-322.
[176] SONG J J, LIU J, TOLIA N H, et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes [J]. Nature Structural & Molecular Biology, 2003, 10(12): 1026-1032.
[177] ELKAYAM E, KUHN C D, TOCILJ A, et al. The structure of human argonaute-2 in complex with miR-20a [J]. Cell, 2012, 150(1): 100-110.
[178] MATSUMOTO N, NISHIMASU H, SAKAKIBARA K, et al. Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA [J]. Cell, 2016, 167(2): 484-497.
[179] BAI X C, MCMULLAN G, SCHERES S H. How cryo-EM is revolutionizing structural biology [J]. Trends in Biochemical Sciences, 2015, 40(1): 49-57.
[180] SGRO G G, COSTA T R D. Cryo-EM Grid Preparation of Membrane Protein Samples for Single Particle Analysis [J]. Frontiers in Molecular Biosciences, 2018, 5: 74.
[181] CREGG J M, TOLSTORUKOV I, KUSARI A, et al. Expression in the yeast Pichia pastoris [J]. Methods in Enzymology, 2009, 463: 169-189.
[182] DUROCHER Y, PERRET S, KAMEN A. High-level and high-throughput recombinant protein production by transient transfection of suspension-growing human 293-EBNA1 cells [J]. Nucleic Acids Research, 2002, 30(2): E9.
[183] UNGER T, PELEG Y. Recombinant protein expression in the baculovirus-infected insect cell system [J]. Methods in Molecular Biology, 2012, 800: 187-199.
[184] RUE S M, ANDERSON P W, GAYLORD M R, et al. A High-Throughput System for Transient and Stable Protein Production in Mammalian Cells [J]. Methods in Molecular Biology, 2019, 2025: 93-142.
[185] BANDARANAYAKE A D, ALMO S C. Recent advances in mammalian protein production [J]. FEBS Letters, 2014, 588(2): 253-260.
[186] BOS A B, LUAN P, DUQUE J N, et al. Optimization and automation of an end-to-end high throughput microscale transient protein production process [J]. Biotechnol Bioeng, 2015, 112(9): 1832-1842.
[187] GEISSE S. Reflections on more than 10 years of TGE approaches [J]. Protein Expression and Purification, 2009, 64(2): 99-107.
[188] SHAW G, MORSE S, ARARAT M, et al. Preferential transformation of human neuronal cells by human adenoviruses and the origin of HEK 293 cells [J]. The FASEB Journal, 2002, 16(8): 869-871.
[189] GRAHAM F L, SMILEY J, RUSSELL W C, et al. Characteristics of a human cell line transformed by DNA from human adenovirus type 5 [J]. Journal of General Virology, 1977, 36(1): 59-74.
[190] SUEN K F, TURNER M S, GAO F, et al. Transient expression of an IL-23R extracellular domain Fc fusion protein in CHO vs. HEK cells results in improved plasma exposure [J]. Protein Expression and Purification, 2010, 71(1): 96-102.
[191] CROSET A, DELAFOSSE L, GAUDRY J P, et al. Differences in the glycosylation of recombinant proteins expressed in HEK and CHO cells [J]. Journal of Biotechnology, 2012, 161(3): 336-348.
[192] KIM J Y, KIM Y G, LEE G M. CHO cells in biotechnology for production of recombinant proteins: current state and further potential [J]. Applied Microbiology and Biotechnology, 2012, 93(3): 917-930.
[193] LONGO P A, KAVRAN J M, KIM M S, et al. Transient mammalian cell transfection with polyethylenimine (PEI) [J]. Methods in Enzymology, 2013, 529: 227-240.
[194] LAURENTI D, OOI L. Mammalian expression systems and transfection techniques [J]. Methods in Molecular Biology, 2013, 998: 21-32.
[195] BOUSSIF O, LEZOUALC'H F, ZANTA M A, et al. A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine [J]. proceedings of the national academy of sciences, 1995, 92(16): 7297-7301.
[196] HAO F, LI Y, ZHU J, et al. Polyethylenimine-based Formulations for Delivery of Oligonucleotides [J]. Current Medicinal Chemistry, 2019, 26(13): 2264-2284.
[197] SONAWANE N D, SZOKA F C, JR., VERKMAN A S. Chloride accumulation and swelling in endosomes enhances DNA transfer by polyamine-DNA polyplexes [J]. Journal of Biological Chemistry, 2003, 278(45): 44826-44831.
[198] PARIS S, BURLACU A, DUROCHER Y. Opposing roles of syndecan-1 and syndecan-2 in polyethyleneimine-mediated gene delivery [J]. Journal of Biological Chemistry, 2008, 283(12): 7697-7704.
[199] PAYNE C K, JONES S A, CHEN C, et al. Internalization and trafficking of cell surface proteoglycans and proteoglycan-binding ligands [J]. Traffic, 2007, 8(4): 389-401.
[200] KOPATZ I, REMY J S, BEHR J P. A model for non-viral gene delivery: through syndecan adhesion molecules and powered by actin [J]. The Journal of Gene Medicine, 2004, 6(7): 769-776.
[201] ZHAO Y, BISHOP B, CLAY J E, et al. Automation of large scale transient protein expression in mammalian cells [J]. Journal of Structural Biology, 2011, 175(2): 209-215.
[202] POSSEE R D. Baculoviruses as expression vectors [J]. Current Opinion in Biotechnology, 1997, 8(5): 569-572.
[203] MILLER L K. Baculoviruses as Gene-Expression Vectors [J]. Annual Review of Microbiology, 1988, 42: 177-199.
[204] KIDD I M, EMERY V C. The Use of Baculoviruses as Expression Vectors [J]. Applied Biochemistry and Biotechnology, 1993, 42(2-3): 137-159.
[205] ATKINSON A E, WEITZMAN M D, OBOSI L, et al. Baculoviruses as Vectors for Foreign Gene-Expression in Insect Cells [J]. pesticide science, 1990, 28(2): 215-224.
[206] FRASER M J. Ultrastructural Observations of Virion Maturation in Autographa-Californica Nuclear Polyhedrosis-Virus Infected Spodoptera-Frugiperda Cell-Cultures [J]. Journal of Molecular Structure, 1986, 95(1-3): 189-195.
[207] SHANG H, GARRETSON T A, KUMAR C M S, et al. Improved pFastBac (TM) donor plasmid vectors for higher protein production using the Bac-to-Bac (R) baculovirus expression vector system [J]. Journal of Biotechnology, 2017, 255: 37-46.
[208] VAUGHN J L, GOODWIN R H, TOMPKINS G J, et al. The establishment of two cell lines from the insect Spodoptera frugiperda (Lepidoptera; Noctuidae) [J]. In Vitro, 1977, 13(4): 213-217.
[209] JARVIS D L. Baculovirus-insect cell expression systems [J]. Methods in Enzymology, 2009, 463: 191-222.
[210] LUCKOW V A, LEE S C, BARRY G F, et al. Efficient Generation of Infectious Recombinant Baculoviruses by Site-Specific Transposon-Mediated Insertion of Foreign Genes into a Baculovirus Genome Propagated in Escherichia-Coli [J]. Journal of Virology, 1993, 67(8): 4566-4579.
[211] VIALARD J E, RICHARDSON C D. The 1,629-nucleotide open reading frame located downstream of the Autographa californica nuclear polyhedrosis virus polyhedrin gene encodes a nucleocapsid-associated phosphoprotein [J]. JOURNAL OF VIROLOGY, 1993, 67(10): 5859-5866.
[212] ADENIYI A A, LUA L H. Protein Expression in the Baculovirus-Insect Cell Expression System [J]. Methods in Molecular Biology, 2020, 2073: 17-37.
[213] SARI D, GUPTA K, THIMIRI GOVINDA RAJ D B, et al. The MultiBac Baculovirus/Insect Cell Expression Vector System for Producing Complex Protein Biologics [J]. Advances in Experimental Medicine and Biology, 2016, 896: 199-215.
[214] JENSEN I S, INUI K, DRAKULIC S, et al. Expression of Flp Protein in a Baculovirus/Insect Cell System for Biotechnological Applications [J]. The Protein Journal, 2017, 36(4): 332-342.
[215] MASOOMI DEZFOOLI S, TAN W S, TEY B T, et al. Expression and purification of the matrix protein of Nipah virus in baculovirus insect cell system [J]. Biotechnology Progress, 2016, 32(1): 171-177.
[216] MAHAJAN P, STRAIN-DAMERELL C, GILEADI O, et al. Medium-throughput production of recombinant human proteins: protein production in insect cells [J]. Methods in Molecular Biology, 2014, 1091: 95-121.
[217] SHI Y G. A Glimpse of Structural Biology through X-Ray Crystallography [J]. Cell, 2014, 159(5): 995-1014.
[218] WATSON J D, CRICK F H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid [J]. Nature, 1953, 171(4356): 737-738.
[219] KENDREW J C, BODO G, DINTZIS H M, et al. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis [J]. Nature, 1958, 181(4610): 662-666.
[220] KENDREW J C, DICKERSON R E, STRANDBERG B E, et al. Structure of myoglobin: A three-dimensional Fourier synthesis at 2 A. resolution [J]. Nature, 1960, 185(4711): 422-427.
[221] BAX A, CLORE G M. Protein NMR: Boundless opportunities [J]. Journal of Magnetic Resonance, 2019, 306: 187-191.
[222] RANKIN N J, PREISS D, WELSH P, et al. The emergence of proton nuclear magnetic resonance metabolomics in the cardiovascular arena as viewed from a clinical perspective [J]. Atherosclerosis, 2014, 237(1): 287-300.
[223] EARL L A, FALCONIERI V, MILNE J L, et al. Cryo-EM: beyond the microscope [J]. Current Opinion in Structural Biology, 2017, 46: 71-78.
[224] CHENG Y F. Single-particle cryo-EM-How did it get here and where will it go [J]. Science, 2018, 361(6405): 876-880.
[225] NOGALES E. The development of cryo-EM into a mainstream structural biology technique [J]. Nature Methods, 2016, 13(1): 24-27.
[226] CALLAWAY E. The revolution will not be crystallized: a new method sweeps through structural biology [J]. Nature, 2015, 525(7568): 172-174.
[227] FRANK J. Averaging of low exposure electron micrographs of non-periodic objects [J]. Ultramicroscopy, 1975, 1(2): 159-162.
[228] DEROSIER D J, KLUG A. Structure of the tubular variants of the head of bacteriophage T4 (polyheads). I. Arrangement of subunits in some classes of polyheads [J]. Journal of Molecular Biology, 1972, 65(3): 469-488.
[229] BAKER L A, RUBINSTEIN J L. Radiation damage in electron cryomicroscopy [J]. Methods in Enzymology, 2010, 481: 371-388.
[230] DANEV R, YANAGISAWA H, KIKKAWA M. Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions [J]. Trends in Biochemical Sciences, 2019, 44(10): 837-848.
[231] FRANK J. Single-particle imaging of macromolecules by cryo-electron microscopy [J]. Annual Review of Biophysics and Biomolecular Structure, 2002, 31: 303-319.
[232] DE ROSIER D J, KLUG A. Reconstruction of three dimensional structures from electron micrographs [J]. Nature, 1968, 217(5124): 130-134.
[233] FRANK J. Single-Particle Reconstruction of Biological Molecules-Story in a Sample (Nobel Lecture) [J]. Angewandte Chemie - International Edition, 2018, 57(34): 10826-10841.
[234] CHENG Y, GRIGORIEFF N, PENCZEK P A, et al. A primer to single-particle cryo-electron microscopy [J]. Cell, 2015, 161(3): 438-449.
[235] ZHOU J, CHIZHIK A I, CHU S, et al. Single-particle spectroscopy for functional nanomaterials [J]. Nature, 2020, 579(7797): 41-50.
[236] SKINIOTIS G, SOUTHWORTH D R. Single-particle cryo-electron microscopy of macromolecular complexes [J]. Microscopy , 2016, 65(1): 9-22.
[237] THOMPSON R F, WALKER M, SIEBERT C A, et al. An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology [J]. Methods, 2016, 100: 3-15.
[238] PASSMORE L A, RUSSO C J. Specimen Preparation for High-Resolution Cryo-EM [J]. Methods in Enzymology, 2016, 579: 51-86.
[239] GALLAGHER J R, KIM A J, GULATI N M, et al. Negative-Stain Transmission Electron Microscopy of Molecular Complexes for Image Analysis by 2D Class Averaging [J]. Current Protocols in Microbiology, 2019, 54(1): e90.
[240] KISELEV N A, SHERMAN M B, TSUPRUN V L. Negative staining of proteins [J]. Electron Microscopy Reviews, 1990, 3(1): 43-72.
[241] OHI M, LI Y, CHENG Y, et al. Negative Staining and Image Classification - Powerful Tools in Modern Electron Microscopy [J]. Biological Procedures Online, 2004, 6: 23-34.
[242] BRENNER S, HORNE R W. A negative staining method for high resolution electron microscopy of viruses [J]. Biochimica et Biophysica Acta, 1959, 34: 103-110.
[243] FRANK J, GOLDFARB W, EISENBERG D, et al. Reconstruction of glutamine synthetase using computer averaging [J]. Ultramicroscopy, 1978, 3(3): 283-290.
[244] SCARFF C A, FULLER M J G, THOMPSON R F, et al. Variations on Negative Stain Electron Microscopy Methods: Tools for Tackling Challenging Systems [J]. Jove-Journal of Visualized Experiments, 2018, (132): 57199.
[245] BRILLAULT L, LANDSBERG M J. Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy [J]. Methods in Molecular Biology, 2020, 2073: 221-246.
[246] HENDERSON R. The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules [J]. Quarterly Reviews of Biophysics, 1995, 28(2): 171-193.
[247] GLAESER R M. Limitations to significant information in biological electron microscopy as a result of radiation damage [J]. Journal of Ultrastructure Research, 1971, 36(3): 466-482.
[248] GLAESER R M. Prospects for extending the resolution limit of the electron microscope [J]. Journal of Microscopy, 1979, 117(1): 77-91.
[249] ADRIAN M, DUBOCHET J, LEPAULT J, et al. Cryo-electron microscopy of viruses [J]. Nature, 1984, 308(5954): 32-36.
[250] DUBOCHET J, CHANG J J, FREEMAN R, et al. Frozen Aqueous Suspensions [J]. Ultramicroscopy, 1982, 10(1-2): 55-61.
[251] TAYLOR K A, GLAESER R M. Electron diffraction of frozen, hydrated protein crystals [J]. Science, 1974, 186(4168): 1036-1037.
[252] BAMMES B E, JAKANA J, SCHMID M F, et al. Radiation damage effects at four specimen temperatures from 4 to 100 K [J]. Journal of Structural Biology, 2010, 169(3): 331-341.
[253] HENDERSON R. Cryoprotection of Protein Crystals against Radiation-Damage in Electron and X-Ray-Diffraction [J]. Proceedings of The Royal Society B-Biological Sciences, 1990, 241(1300): 6-8.
[254] WEISSENBERGER G, HENDERIKX R J M, PETERS P J. Understanding the invisible hands of sample preparation for cryo-EM [J]. Nature Methods, 2021, 18(5): 463-471.
[255] RHEINBERGER J, OOSTERGETEL G, RESCH G P, et al. Optimized cryo-EM data-acquisition workflow by sample-thickness determination [J]. Acta Crystallographica Section D: Structural Biology, 2021, 77(Pt 5): 565-571.
[256] MOONEY P. Optimization of image collection for cellular electron microscopy [J]. Methods in Cell Biology, 2007, 79: 661-719.
[257] SULOWAY C, PULOKAS J, FELLMANN D, et al. Automated molecular microscopy: the new Leginon system [J]. Journal of Structural Biology, 2005, 151(1): 41-60.
[258] LIAO M, CAO E, JULIUS D, et al. Structure of the TRPV1 ion channel determined by electron cryo-microscopy [J]. Nature, 2013, 504(7478): 107-112.
[259] MCMULLAN G, FARUQI A R, HENDERSON R. Direct Electron Detectors [J]. Methods in Enzymology, 2016, 579: 1-17.
[260] BRILOT A F, CHEN J Z, CHENG A, et al. Beam-induced motion of vitrified specimen on holey carbon film [J]. Journal of Structural Biology, 2012, 177(3): 630-637.
[261] SCHERES S H. RELION: implementation of a Bayesian approach to cryo-EM structure determination [J]. Journal of Structural Biology, 2012, 180(3): 519-530.
[262] SCHERES S H. A Bayesian view on cryo-EM structure determination [J]. Journal of Molecular Biology, 2012, 415(2): 406-418.
[263] SCAPIN G, PROSISE W W, WISMER M K, et al. A novel storage system for cryoEM samples [J]. Journal of Structural Biology, 2017, 199(1): 84-86.
[264] SCHERES S H W. Amyloid structure determination in RELION-3.1 [J]. Acta Crystallographica Section D: Structural Biology, 2020, 76(Pt 2): 94-101.
[265] ZIVANOV J, NAKANE T, FORSBERG B O, et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3 [J]. Elife, 2018, 7: e42166.
[266] ZHENG S Q, PALOVCAK E, ARMACHE J P, et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy [J]. Nature Methods, 2017, 14(4): 331-332.
[267] ROHOU A, GRIGORIEFF N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs [J]. Journal of Structural Biology, 2015, 192(2): 216-221.
[268] SU M. goCTF: Geometrically optimized CTF determination for single-particle cryo-EM [J]. Journal of Structural Biology, 2019, 205(1): 22-29.
[269] EMSLEY P, LOHKAMP B, SCOTT W G, et al. Features and development of Coot [J]. Acta Crystallographica Section D: Biological Crystallography, 2010, 66(Pt 4): 486-501.
[270] AFONINE P V, POON B K, READ R J, et al. Real-space refinement in PHENIX for cryo-EM and crystallography [J]. Acta Crystallographica Section D: Structural Biology, 2018, 74(Pt 6): 531-544.
[271] ADAMS P D, AFONINE P V, BUNKOCZI G, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution [J]. Acta Crystallographica Section D: Biological Crystallography, 2010, 66(Pt 2): 213-221.
[272] PETTERSEN E F, GODDARD T D, HUANG C C, et al. UCSF Chimera--a visualization system for exploratory research and analysis [J]. Journal of Computational Chemistry, 2004, 25(13): 1605-1612.
[273] LIN B, MENG H, BING H, et al. Efficient expression of acetylcholine-binding protein from Aplysia californica in Bac-to-Bac system [J]. BioMed Research International, 2014, 2014: 691480.
[274] RAMACHANDRAN V, CHEN X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis [J]. Science, 2008, 321(5895): 1490-1492.
[275] LI J, YANG Z, YU B, et al. Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis [J]. Current Biology, 2005, 15(16): 1501-1507.
[276] HUANG R H. Unique 2'-O-methylation by Hen1 in eukaryotic RNA interference and bacterial RNA repair [J]. Biochemistry, 2012, 51(20): 4087-4095.
[277] HUANG Y, JI L J, HUANG Q C, et al. Structural insights into mechanisms of the small RNA methyltransferase HEN1 [J]. Nature, 2009, 461(7265): 823-827.
[278] YU B, YANG Z Y, LI J J, et al. Methylation as a crucial step in plant microRNA biogenesis [J]. Science, 2005, 307(5711): 932-935.
[279] YANG Z Y, EBRIGHT Y W, YU B, et al. HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2 ' OH of the 3 ' terminal nucleotide [J]. Nucleic Acids Research, 2006, 34(2): 667-675.
[280] ABOU ELELA S, JI X. Structure and function of Rnt1p: An alternative to RNAi for targeted RNA degradation [J]. Wiley Interdisciplinary Reviews-RNA, 2019, 10(3): e1521.
[281] SONG H, FANG X, JIN L, et al. The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III [J]. Structure, 2017, 25(2): 353-363.
修改评论