Aagaard,, L., Zhang,, J., von Eije,, K. J., Li,, H., Sœtrom,, P., Amarzguioui,, M., & Rossi,, J. J. (2008). Engineering and optimization of the mir‐106b‐cluster for ectopic expression of multiplexed anti‐HIV RNAs. Gene Therapy, 15(23), 1536–1549. https://doi.org/10.1038/gt.2008.147
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 Research, 33(8), 2697–2706. https://doi.org/10.1093/nar/gki567
Andersson,, M. G., Haasnoot,, P. C. J., Xu,, N., Berenjian,, S., Berkhout,, B., & Akusjärvi,, G. (2005). Suppression of RNA interference by adenovirus virus‐associated RNA. Journal of Virology, 79(15), 9556–9565. https://doi.org/10.1128/JVI.79.15.9556-9565.2005
Ashizawa,, T., Öz,, G., & Paulson,, H. L. (2018). Spinocerebellar ataxias: Prospects and challenges for therapy development. Nature Reviews. Neurology, 14(10), 590–605. https://doi.org/10.1038/s41582-018-0051-6
Auyeung,, V. C., Ulitsky,, I., McGeary,, S. E., & Bartel,, D. P. (2013). Beyond secondary structure: Primary‐sequence determinants license pri‐miRNA hairpins for processing. Cell, 152(4), 844–858. https://doi.org/10.1016/j.cell.2013.01.031
Baek,, M. N., Jung,, K. H., Halder,, D., Choi,, M. R., Lee,, B.‐H., Lee,, B.‐C., Jung,, M. H., Choi,, I.‐G., Chung,, M.‐K., Oh,, D.‐Y., & Chai,, Y. G. (2010). Artificial microRNA‐based neurokinin‐1 receptor gene silencing reduces alcohol consumption in mice. Neuroscience Letters, 475(3), 124–128. https://doi.org/10.1016/j.neulet.2010.03.051
Bartel,, D. P. (2004). MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116(2), 281–297. https://doi.org/10.1016/s0092-8674(04)00045-5
Bartel,, D. P. (2018). Metazoan MicroRNAs. Cell, 173(1), 20–51. https://doi.org/10.1016/j.cell.2018.03.006
Bauer,, M., Kinkl,, N., Meixner,, A., Kremmer,, E., Riemenschneider,, M., Förstl,, H., Gasser,, T., & Ueffing,, M. (2009). Prevention of interferon‐stimulated gene expression using microRNA‐designed hairpins. Gene Therapy, 16(1), 142–147. https://doi.org/10.1038/gt.2008.123
Bisset,, D. R., Stepniak‐Konieczna,, E. A., Zavaljevski,, M., Wei,, J., Carter,, G. T., Weiss,, M. D., & Chamberlain,, J. R. (2015). Therapeutic impact of systemic AAV‐mediated RNA interference in a mouse model of myotonic dystrophy. Human Molecular Genetics, 24(17), 4971–4983. https://doi.org/10.1093/hmg/ddv219
Bonetta,, A., Mailly,, L., Robinet,, E., Travé,, G., Masson,, M., & Deryckere,, F. (2015). Artificial microRNAs against the viral E6 protein provoke apoptosis in HPV positive cancer cells. Biochemical and Biophysical Research Communications. 465, 658–664. https://doi.org/10.1016/j.bbrc.2015.07.144
Borel,, F., Gernoux,, G., Cardozo,, B., Metterville,, J. P., Toro Cabreja,, G. C., Song,, L., Su,, Q., Gao,, G. P., Elmallah,, M. K., Brown,, R. H., & Mueller,, C. (2016). Therapeutic rAAVrh10 mediated SOD1 silencing in adult SOD1G93A mice and nonhuman Primates. Human Gene Therapy, 27(1), 19–31. https://doi.org/10.1089/hum.2015.122
Borel,, F., Gernoux,, G., Sun,, H., Stock,, R., Blackwood,, M., Brown,, R. H., & Mueller,, C. (2018). Safe and effective superoxide dismutase 1 silencing using artificial microRNA in macaques. Science Translational Medicine, 10(465), eaau6414. https://doi.org/10.1126/scitranslmed.aau6414
Boudreau,, R., Martins,, I., & Davidson,, B. L. (2009). Artificial microRNAs as siRNA shuttles: Improved safety as compared to shRNAs in vitro and in vivo. Molecular Therapy: The Journal of the American Society of Gene Therapy, 17(1), 169–175. https://doi.org/10.1038/mt.2008.231
Boudreau,, R. L., McBride,, J. L., Martins,, I., Shen,, S., Xing,, Y., Carter,, B. J., & Davidson,, B. L. (2009). Nonallele‐specific silencing of mutant and wild‐type Huntingtin demonstrates therapeutic efficacy in Huntington`s disease mice. Molecular Therapy: The Journal of the American Society of Gene Therapy, 17(6), 1053–1063. https://doi.org/10.1038/mt.2009.17
Boudreau,, R. L., Monteys,, A. M., & Davidson,, B. L. (2008). Minimizing variables among hairpin‐based RNAi vectors reveals the potency of shRNAs. RNA, 14(9), 1834–1844. https://doi.org/10.1261/rna.1062908
Brendel,, C., Guda,, S., Renella,, R., Bauer,, D. E., Canver,, M. C., Kim,, Y.‐J., Heeney,, M. M., Klatt,, D., Fogel,, J., Milsom,, M. D., Orkin,, S. H., Gregory,, R. I., & Williams,, D. A. (2016). Lineage‐specific BCL11A knockdown circumvents toxicities and reverses sickle phenotype. The Journal of Clinical Investigation, 126(10), 3868–3878. https://doi.org/10.1172/JCI87885
Brendel,, C., Negre,, O., Rothe,, M., Guda,, S., Parsons,, G., Harris,, C., McGuinness,, M., Abriss,, D., Tsytsykova,, A., Klatt,, D., Bentler,, M., Pellin,, D., Christiansen,, L., Schambach,, A., Manis,, J., Trebeden‐Negre,, H., Bonner,, M., Esrick,, E., Veres,, G., … Williams,, D. A. (2020). Preclinical evaluation of a novel lentiviral vector driving lineage‐specific BCL11A knockdown for sickle cell gene therapy. Molecular Therapy—Methods %26 Clinical Development, 17, 589–600. https://doi.org/10.1016/j.omtm.2020.03.015
Buijsen,, R. A. M., Toonen,, L. J. A., Gardiner,, S. L., & van Roon‐Mom,, W. M. C. (2019). Genetics, mechanisms, and therapeutic progress in polyglutamine spinocerebellar ataxias. Neurotherapeutics: The Journal of the American Society for Experimental NeuroTherapeutics, 16(2), 263–286. https://doi.org/10.1007/s13311-018-00696-y
Cai,, X., Hagedorn,, C. H., & Cullen,, B. R. (2004). Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA (New York, N.Y.), 10(12), 1957–1966. https://doi.org/10.1261/rna.7135204
Calloni,, R., & Bonatto,, D. (2015). Scaffolds for artificial miRNA expression in animal cells. Human Gene Therapy Methods, 26(5), 162–174. https://doi.org/10.1089/hgtb.2015.043
Carbonell,, A., & Daròs,, J.‐A. (2019). Design, synthesis, and functional analysis of highly specific artificial small RNAs with antiviral activity in plants. Methods in Molecular Biology (Clifton, N.J.), 2028, 231–246. https://doi.org/10.1007/978-1-4939-9635-3_13
Chang,, K., Elledge,, S. J., & Hannon,, G. J. (2006). Lessons from nature: MicroRNA‐based shRNA libraries. Nature Methods, 3(9), 707–714. https://doi.org/10.1038/nmeth923
Cheloufi,, S., Dos Santos,, C. O., Chong,, M. M. W., & Hannon,, G. J. (2010). A Dicer‐independent miRNA biogenesis pathway that requires ago catalysis. Nature, 465(7298), 584–589. https://doi.org/10.1038/nature09092
Chen,, H.‐H., Mack,, L. M., Kelly,, R., Ontell,, M., Kochanek,, S., & Clemens,, P. R. (1997). Persistence in muscle of an adenoviral vector that lacks all viral genes. Proceedings of the National Academy of Sciences of the United States of America, 94(5), 1645–1650.
Chen,, J.‐F., Mandel,, E. M., Thomson,, J. M., Wu,, Q., Callis,, T. E., Hammond,, S. M., Conlon,, F. L., & Wang,, D.‐Z. (2006). The role of microRNA‐1 and microRNA‐133 in skeletal muscle proliferation and differentiation. Nature Genetics, 38(2), 228–233. https://doi.org/10.1038/ng1725
Chen,, S. C.‐Y., Stern,, P., Guo,, Z., & Chen,, J. (2011). Expression of multiple artificial microRNAs from a chicken miRNA126‐based lentiviral vector. PLoS One, 6(7), e22437. https://doi.org/10.1371/journal.pone.0022437
Chendrimada,, T. P., Gregory,, R. I., 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(7051), 740–744. https://doi.org/10.1038/nature03868
Choi,, J.‐G., Bharaj,, P., Abraham,, S., Ma,, H., Yi,, G., Ye,, C., Dang,, Y., Manjunath,, N., Wu,, H., & Shankar,, P. (2015). Multiplexing seven miRNA‐based shRNAs to suppress HIV replication. Molecular Therapy, 23(2), 310–320. https://doi.org/10.1038/mt.2014.205
Chung,, K.‐H., Hart,, C. C., Al‐Bassam,, S., Avery,, A., Taylor,, J., Patel,, P. D., Vojtek,, A. B., & Turner,, D. L. (2006). Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR‐155. Nucleic Acids Research, 34(7), e53. https://doi.org/10.1093/nar/gkl143
Concepcion,, C. P., Bonetti,, C., & Ventura,, A. (2012). The miR‐17‐92 family of microRNA clusters in development and disease. Cancer Journal (Sudbury, Mass.), 18(3), 262–267. https://doi.org/10.1097/PPO.0b013e318258b60a
Daya,, S., & Berns,, K. I. (2008). Gene therapy using Adeno‐associated virus vectors. Clinical Microbiology Reviews, 21(4), 583–593. https://doi.org/10.1128/CMR.00008-08
Dhungel,, B. P., Bailey,, C. G., & Rasko,, J. E. J. (2020). Journey to the center of the cell: Tracing the path of AAV transduction. Trends in Molecular Medicine. https://doi.org/10.1016/j.molmed.2020.09.010
Dickins,, R. A., Hemann,, M. T., Zilfou,, J. T., Simpson,, D. R., Ibarra,, I., Hannon,, G. J., & Lowe,, S. W. (2005). Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nature Genetics, 37(11), 1289–1295. https://doi.org/10.1038/ng1651
Dore,, L. C., Amigo,, J. D., dos Santos,, C. O., Zhang,, Z., Gai,, X., Tobias,, J. W., Yu,, D., Klein,, A. M., Dorman,, C., Wu,, W., Hardison,, R. C., Paw,, B. H., & Weiss,, M. J. (2008). A GATA‐1‐regulated microRNA locus essential for erythropoiesis. Proceedings of the National Academy of Sciences of the United States of America, 105(9), 3333–3338. https://doi.org/10.1073/pnas.0712312105
Du,, G., Yonekubo,, J., Zeng,, Y., Osisami,, M., & Frohman,, M. A. (2006). Design of expression vectors for RNA interference based on miRNAs and RNA splicing. The FEBS Journal, 273(23), 5421–5427. https://doi.org/10.1111/j.1742-4658.2006.05534.x
Dufour,, B. D., Smith,, C. A., Clark,, R. L., Walker,, T. R., & McBride,, J. L. (2014). Intrajugular vein delivery of AAV9‐RNAi prevents neuropathological changes and weight loss in Huntington`s disease mice. Molecular Therapy, 22(4), 797–810. https://doi.org/10.1038/mt.2013.289
Duyao,, M., Ambrose,, C., Myers,, R., Novelletto,, A., Persichetti,, F., Frontali,, M., Folstein,, S., Ross,, C., Franz,, M., & Abbott,, M. (1993). Trinucleotide repeat length instability and age of onset in Huntington`s disease. Nature Genetics, 4(4), 387–392. https://doi.org/10.1038/ng0893-387
Elbashir,, S. M., Lendeckel,, W., & Tuschl,, T. (2001). RNA interference is mediated by 21‐ and 22‐nucleotide RNAs. Genes %26 Development, 15(2), 188–200.
Ely,, A., Naidoo,, T., & Arbuthnot,, P. (2009). Efficient silencing of gene expression with modular trimeric Pol II expression cassettes comprising microRNA shuttles. Nucleic Acids Research, 37(13), e91. https://doi.org/10.1093/nar/gkp446
Ely,, A., Naidoo,, T., Mufamadi,, S., Crowther,, C., & Arbuthnot,, P. (2008). Expressed anti‐HBV primary microRNA shuttles inhibit viral replication efficiently in vitro and in vivo. Molecular Therapy: The Journal of the American Society of Gene Therapy, 16(6), 1105–1112. https://doi.org/10.1038/mt.2008.82
Evers,, M., Miniarikova,, J., Juhas,, S., Vallès,, A., Bohuslavova,, B., Juhasova,, J., Skalnikova,, H. K., Vodicka,, P., Valekova,, I., Brouwers,, C., Blits,, B., Lubelski,, J., Kovarova,, H., Ellederova,, Z., van Deventer,, S. J., Petry,, H., Motlik,, J., & Konstantinova,, P. (2018). AAV5‐miHTT gene therapy demonstrates broad distribution and strong human mutant Huntingtin lowering in a Huntington`s disease Minipig model. Molecular Therapy: The Journal of the American Society of Gene Therapy, 26(9), 2163–2177. https://doi.org/10.1016/j.ymthe.2018.06.021
Fan,, Z.‐D., Zhang,, L., Shi,, Z., Gan,, X.‐B., Gao,, X.‐Y., & Zhu,, G.‐Q. (2012). Artificial microRNA interference targeting AT 1a receptors in paraventricular nucleus attenuates hypertension in rats. Gene Therapy, 19(8), 810–817. https://doi.org/10.1038/gt.2011.145
Fang,, W., & Bartel,, D. P. (2015). The menu of features that define primary microRNAs and enable de novo design of microRNA genes. Molecular Cell, 60(1), 131–145. https://doi.org/10.1016/j.molcel.2015.08.015
Faraoni,, I., Antonetti,, F. R., Cardone,, J., & Bonmassar,, E. (2009). miR‐155 gene: A typical multifunctional microRNA. Biochimica et Biophysica Acta (BBA) ‐ Molecular Basis of Disease, 1792(6), 497–505. https://doi.org/10.1016/j.bbadis.2009.02.013
Fellmann,, C., Hoffmann,, T., Sridhar,, V., Hopfgartner,, B., Muhar,, M., Roth,, M., Lai,, D. Y., Barbosa,, I. A. M., Kwon,, J. S., Guan,, Y., Sinha,, N., & Zuber,, J. (2013). An optimized microRNA backbone for effective single‐copy RNAi. Cell Reports, 5(6), 1704–1713. https://doi.org/10.1016/j.celrep.2013.11.020
Galka‐Marciniak,, P., Olejniczak,, M., Starega‐Roslan,, J., Szczesniak,, M. W., Makalowska,, I., & Krzyzosiak,, W. J. (2016). SiRNA release from pri‐miRNA scaffolds is controlled by the sequence and structure of RNA. Biochimica et Biophysica Acta (BBA) ‐ Gene Regulatory Mechanisms, 1859(4), 639–649. https://doi.org/10.1016/j.bbagrm.2016.02.014
Gao,, Y.‐F., Yu,, L., Wei,, W., Li,, J.‐B., Luo,, Q.‐L., & Shen,, J.‐L. (2008). Inhibition of hepatitis B virus gene expression and replication by artificial microRNA. World Journal of Gastroenterology: WJG, 14(29), 4684–4689. https://doi.org/10.3748/wjg.14.4684
Girardi,, E., López,, P., & Pfeffer,, S. (2018). On the importance of host MicroRNAs during viral infection. Frontiers in Genetics, 9, 439. https://doi.org/10.3389/fgene.2018.00439
Grishok,, A., Pasquinelli,, A. E., Conte,, D., Li,, N., Parrish,, S., Ha,, I., Baillie,, D. L., Fire,, A., Ruvkun,, G., & Mello,, C. C. (2001). Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106(1), 23–34. https://doi.org/10.1016/s0092-8674(01)00431-7
Größl,, T., Hammer,, E., Bien‐Möller,, S., Geisler,, A., Pinkert,, S., Röger,, C., Poller,, W., Kurreck,, J., Völker,, U., Vetter,, R., & Fechner,, H. (2014). A novel artificial MicroRNA expressing AAV vector for phospholamban silencing in cardiomyocytes improves Ca2+ uptake into the sarcoplasmic reticulum. PLoS One, 9(3), e92188. https://doi.org/10.1371/journal.pone.0092188
Guda,, S., Brendel,, C., Renella,, R., Du,, P., Bauer,, D. E., Canver,, M. C., Grenier,, J. K., Grimson,, A. W., Kamran,, S. C., Thornton,, J., de Boer,, H., Root,, D. E., Milsom,, M. D., Orkin,, S. H., Gregory,, R. I., & Williams,, D. A. (2015). MiRNA‐embedded shRNAs for lineage‐specific BCL11A knockdown and hemoglobin F induction. Molecular Therapy: The Journal of the American Society of Gene Therapy, 23(9), 1465–1474. https://doi.org/10.1038/mt.2015.113
Ha,, M., & Kim,, V. N. (2014). Regulation of microRNA biogenesis. Nature Reviews Molecular Cell Biology, 15(8), 509–524. https://doi.org/10.1038/nrm3838
Han,, J., Lee,, Y., Yeom,, K.‐H., Kim,, Y.‐K., Jin,, H., & Kim,, V. N. (2004). The Drosha‐DGCR8 complex in primary microRNA processing. Genes %26 Development, 18(24), 3016–3027. https://doi.org/10.1101/gad.1262504
Han,, J., Lee,, Y., Yeom,, K.‐H., Nam,, J.‐W., Heo,, I., Rhee,, J.‐K., Sohn,, S. Y., Cho,, Y., Zhang,, B.‐T., & Kim,, V. N. (2006). Molecular basis for the recognition of primary microRNAs by the Drosha‐DGCR8 complex. Cell, 125(5), 887–901. https://doi.org/10.1016/j.cell.2006.03.043
Herrera‐Carrillo,, E., Liu,, Y. P., & Berkhout,, B. (2017). Improving miRNA delivery by optimizing miRNA expression cassettes in diverse virus vectors. Human Gene Therapy Methods, 28(4), 177–190. https://doi.org/10.1089/hgtb.2017.036
Huang,, J., Mei,, H., Tang,, Z., Li,, J., Zhang,, X., Lu,, Y., Huang,, F., Jin,, Q., & Wang,, Z. (2017). Triple‐amiRNA VEGFRs inhibition in pancreatic cancer improves the efficacy of chemotherapy through EMT regulation. Journal of Controlled Release, 245, 1–14. https://doi.org/10.1016/j.jconrel.2016.11.024
Huang,, X., & Jia,, Z. (2013). Construction of HCC‐targeting artificial miRNAs using natural miRNA precursors. Experimental and Therapeutic Medicine, 6(1), 209–215. https://doi.org/10.3892/etm.2013.1111
Hutvágner,, G., McLachlan,, J., Pasquinelli,, A. E., Bálint,, E., Tuschl,, T., & Zamore,, P. D. (2001). A cellular function for the RNA‐interference enzyme Dicer in the maturation of the let‐7 small temporal RNA. Science (New York, N.Y.), 293(5531), 834–838. https://doi.org/10.1126/science.1062961
Ibrišimović,, M., Kneidinger,, D., Lion,, T., & Klein,, R. (2013). An adenoviral vector‐based expression and delivery system for the inhibition of wild‐type adenovirus replication by artificial microRNAs. Antiviral Research, 97(1), 10–23. https://doi.org/10.1016/j.antiviral.2012.10.008
Ibrišimović,, M., Lion,, T., & Klein,, R. (2013). Combinatorial targeting of 2 different steps in adenoviral DNA replication by herpes simplex virus thymidine kinase and artificial microRNA expression for the inhibition of virus multiplication in the presence of ganciclovir. BMC Biotechnology, 13, 54. https://doi.org/10.1186/1472-6750-13-54
Idogawa,, M., Sasaki,, Y., Suzuki,, H., Mita,, H., Imai,, K., Shinomura,, Y., & Tokino,, T. (2009). A single recombinant adenovirus expressing p53 and p21‐targeting artificial microRNAs efficiently induces apoptosis in human cancer cells. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 15(11), 3725–3732. https://doi.org/10.1158/1078-0432.CCR-08-2396
Iwasaki,, S., Kobayashi,, M., Yoda,, M., Sakaguchi,, Y., Katsuma,, S., Suzuki,, T., & Tomari,, Y. (2010). Hsc70/Hsp90 chaperone machinery mediates ATP‐dependent RISC loading of small RNA duplexes. Molecular Cell, 39(2), 292–299. https://doi.org/10.1016/j.molcel.2010.05.015
Jin,, W., Wang,, J., Liu,, C.‐P., Wang,, H.‐W., & Xu,, R.‐M. (2020). Structural basis for pri‐miRNA recognition by Drosha. Molecular Cell, 78(3), 423–433.e5. https://doi.org/10.1016/j.molcel.2020.02.024
Jopling,, C. (2012). Liver‐specific microRNA‐122. RNA Biology, 9(2), 137–142. https://doi.org/10.4161/rna.18827
Kabekkodu,, S. P., Shukla,, V., Varghese,, V. K., Souza,, J. D., Chakrabarty,, S., & Satyamoorthy,, K. (2018). Clustered miRNAs and their role in biological functions and diseases. Biological Reviews, 93(4), 1955–1986. https://doi.org/10.1111/brv.12428
Karothia,, D., Kumar Dash,, P., Parida,, M., Bhagyawant,, S. S., & Kumar,, J. S. (2020). Vector derived artificial miRNA mediated inhibition of West Nile virus replication and protein expression. Gene, 729, 144300. https://doi.org/10.1016/j.gene.2019.144300
Keeler,, A. M., Sapp,, E., Chase,, K., Sottosanti,, E., Danielson,, E., Pfister,, E., Stoica,, L., DiFiglia,, M., Aronin,, N., & Sena‐Esteves,, M. (2016). Cellular analysis of silencing the Huntington`s disease gene using AAV9 mediated delivery of artificial micro RNA into the striatum of Q140/Q140 mice. Journal of Huntington`s Disease, 5(3), 239–248. https://doi.org/10.3233/JHD-160215
Keiser,, M. S., Boudreau,, R. L., & Davidson,, B. L. (2014). Broad therapeutic benefit after RNAi expression vector delivery to deep cerebellar nuclei: Implications for spinocerebellar ataxia Type 1 therapy. Molecular Therapy, 22(3), 588–595. https://doi.org/10.1038/mt.2013.279
Keiser,, M. S., Geoghegan,, J. C., Boudreau,, R. L., Lennox,, K. A., & Davidson,, B. L. (2013). RNAi or overexpression: Alternative therapies for spinocerebellar ataxia Type 1. Neurobiology of Disease, 56, 6–13. https://doi.org/10.1016/j.nbd.2013.04.003
Keiser,, M. S., Kordower,, J. H., Gonzalez‐Alegre,, P., & Davidson,, B. L. (2015). Broad distribution of ataxin 1 silencing in rhesus cerebella for spinocerebellar ataxia type 1 therapy. Brain, 138(12), 3555–3566. https://doi.org/10.1093/brain/awv292
Keiser,, M. S., Monteys,, A. M., Corbau,, R., Gonzalez‐Alegre,, P., & Davidson,, B. L. (2016). RNAi prevents and reverses phenotypes induced by mutant human ataxin‐1. Annals of Neurology, 80(5), 754–765. https://doi.org/10.1002/ana.24789
Kerr,, A., Tam,, L., Cioroch,, M., Hale,, A., Douglas,, G., Channon,, K., & Wade‐Martins,, R. (2016). A novel combinatorial non‐viral vector to treat familial hypercholesterolaemia (FH). Atherosclerosis, 252, e238. https://doi.org/10.1016/j.atherosclerosis.2016.07.018
Keskin,, S., Brouwers,, C. C., Sogorb‐Gonzalez,, M., Martier,, R., Depla,, J. A., Vallès,, A., van Deventer,, S. J., Konstantinova,, P., & Evers,, M. M. (2019). AAV5‐miHTT lowers Huntingtin mRNA and protein without off‐target effects in patient‐derived neuronal cultures and astrocytes. Molecular Therapy. Methods %26 Clinical Development, 15, 275–284. https://doi.org/10.1016/j.omtm.2019.09.010
Khvorova,, A., Reynolds,, A., & Jayasena,, S. D. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell, 115(2), 209–216. https://doi.org/10.1016/s0092-8674(03)00801-8
Kim,, N., Nguyen,, T. D., Li,, S., & Nguyen,, T. A. (2018). SRSF3 recruits DROSHA to the basal junction of primary microRNAs. RNA, 24(7), 892–898. https://doi.org/10.1261/rna.065862.118
Kim,, Y.‐K., Kim,, B., & Kim,, V. N. (2016). Re‐evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis. Proceedings of the National Academy of Sciences, 113(13), E1881–E1889. https://doi.org/10.1073/pnas.1602532113
Koch,, P., Breuer,, P., Peitz,, M., Jungverdorben,, J., Kesavan,, J., Poppe,, D., Doerr,, J., Ladewig,, J., Mertens,, J., Tüting,, T., Hoffmann,, P., Klockgether,, T., Evert,, B. O., Wüllner,, U., & Brüstle,, O. (2011). Excitation‐induced ataxin‐3 aggregation in neurons from patients with Machado‐Joseph disease. Nature, 480(7378), 543–546. https://doi.org/10.1038/nature10671
Kretov,, D. A., Walawalkar,, I. A., Mora‐Martin,, A., Shafik,, A. M., Moxon,, S., & Cifuentes,, D. (2020). Ago2‐dependent processing allows miR‐451 to evade the global microRNA turnover elicited during erythropoiesis. Molecular Cell, 78(2), 317–328. https://doi.org/10.1016/j.molcel.2020.02.020
Kwon,, S. C., Baek,, S. C., Choi,, Y.‐G., Yang,, J., Lee,, Y.‐S., Woo,, J.‐S., & Kim,, V. N. (2019). Molecular basis for the single‐nucleotide precision of primary microRNA processing. Molecular Cell, 73(3), 505–518.e5. https://doi.org/10.1016/j.molcel.2018.11.005
Lebbink,, R. J., Lowe,, M., Chan,, T., Khine,, H., Wang,, X., & McManus,, M. T. (2011). Polymerase II promoter strength determines efficacy of microRNA adapted shRNAs. PLoS One, 6(10), e26213. https://doi.org/10.1371/journal.pone.0026213
Lee,, Y., Ahn,, C., Han,, J., Choi,, H., Kim,, J., Yim,, J., Lee,, J., Provost,, P., Rådmark,, O., Kim,, S., & Kim,, V. N. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature, 425(6956), 415–419. https://doi.org/10.1038/nature01957
Lee,, Y., Hur,, I., Park,, S.‐Y., Kim,, Y.‐K., Suh,, M. R., & Kim,, V. N. (2006). The role of PACT in the RNA silencing pathway. The EMBO Journal, 25(3), 522–532. https://doi.org/10.1038/sj.emboj.7600942
Lee,, Y., Jeon,, K., Lee,, J.‐T., Kim,, S., & Kim,, V. N. (2002). MicroRNA maturation: Stepwise processing and subcellular localization. The EMBO Journal, 21(17), 4663–4670. https://doi.org/10.1093/emboj/cdf476
Li,, H., Okada,, H., Suzuki,, S., Sakai,, K., Izumi,, H., Matsushima,, Y., Ichinohe,, N., Goto,, Y.‐I., Okada,, T., & Inoue,, K. (2019). Gene suppressing therapy for Pelizaeus‐Merzbacher disease using artificial microRNA. JCI Insight, 4(10). https://doi.org/10.1172/jci.insight.125052
Li,, M., Husic,, N., Lin,, Y., Christensen,, H., Malik,, I., McIver,, S., LaPash Daniels,, C. M., Harris,, D. A., Kotzbauer,, P. T., Goldberg,, M. P., & Snider,, B. J. (2010). Optimal promoter usage for lentiviral vector‐mediated transduction of cultured central nervous system cells. Journal of Neuroscience Methods, 189(1), 56–64. https://doi.org/10.1016/j.jneumeth.2010.03.019
Li,, S., Nguyen,, T. D., Nguyen,, T. L., & Nguyen,, T. A. (2020). Mismatched and wobble base pairs govern primary microRNA processing by human microprocessor. Nature Communications, 11(1), 1926. https://doi.org/10.1038/s41467-020-15674-2
Li,, Z., Wenhua,, Z., Zhao,, W., Baohe,, Z., Yulong,, H., Junsheng,, P., Shirong,, C., & Jinping,, M. (2006). Inhibition of PRL‐3 gene expression in gastric cancer cell line SGC7901 via microRNA suppressed reduces peritoneal metastasis. Biochemical and Biophysical Research Communications, 348, 229–237. https://doi.org/10.1016/j.bbrc.2006.07.043
Liang,, Z., Wu,, H., Reddy,, S., Zhu,, A., Wang,, S., Blevins,, D., Yoon,, Y., Zhang,, Y., & Shim,, H. (2007). Blockade of invasion and metastasis of breast cancer cells via targeting CXCR4 with an artificial microRNA. Biochemical and Biophysical Research Communications. 363, 542–546. https://doi.org/10.1016/j.bbrc.2007.09.007
Liu,, C., Wang,, S., Zhu,, S., Wang,, H., Gu,, J., Gui,, Z., Jing,, J., Hou,, X., & Shao,, Y. (2016). MAP3K1‐targeting therapeutic artificial miRNA suppresses the growth and invasion of breast cancer in vivo and in vitro. Springerplus, 5, 11. https://doi.org/10.1186/s40064-015-1597-z
Liu,, J., Carmell,, M. A., Rivas,, F. V., Marsden,, C. G., Thomson,, J. M., Song,, J.‐J., Hammond,, S. M., Joshua‐Tor,, L., & Hannon,, G. J. (2004). Argonaute2 is the catalytic engine of mammalian RNAi. Science (New York, N.Y.), 305(5689), 1437–1441. https://doi.org/10.1126/science.1102513
Liu,, W., Pfister,, E. L., Kennington,, L. A., Chase,, K. O., Mueller,, C., DiFiglia,, M., & Aronin,, N. (2016). Does the mutant CAG expansion in huntingtin mRNA interfere with exonucleolytic cleavage of its first exon? Journal of Huntington`s Disease, 5(1), 33–38. https://doi.org/10.3233/JHD-150183
Liu,, X., Fang,, H., Chen,, H., Jiang,, X., Fang,, D., Wang,, Y., & Zhu,, D. (2012). An artificial miRNA against HPSE suppresses melanoma invasion properties, correlating with a Down‐regulation of chemokines and MAPK phosphorylation. PLoS One, 7(6), e38659. https://doi.org/10.1371/journal.pone.0038659
Liu,, Y. P., Haasnoot,, J., ter Brake,, O., Berkhout,, B., & Konstantinova,, P. (2008). Inhibition of HIV‐1 by multiple siRNAs expressed from a single microRNA polycistron. Nucleic Acids Research, 36(9), 2811–2824. https://doi.org/10.1093/nar/gkn109
Liu,, Z., Wang,, J., Cheng,, H., Ke,, X., Sun,, L., Zhang,, Q. C., & Wang,, H.‐W. (2018). Cryo‐EM structure of human dicer and its complexes with a pre‐miRNA substrate. Cell, 173(5), 1191–1203.e12. https://doi.org/10.1016/j.cell.2018.03.080
Lu,, S., & Cullen,, B. R. (2004). Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and MicroRNA biogenesis. Journal of Virology, 78(23), 12868–12876. https://doi.org/10.1128/JVI.78.23.12868-12876.2004
Ma,, H., Wu,, Y., Choi,, J.‐G., & Wu,, H. (2013). Lower and upper stem‐single‐stranded RNA junctions together determine the Drosha cleavage site. Proceedings of the National Academy of Sciences of the United States of America, 110(51), 20687–20692. https://doi.org/10.1073/pnas.1311639110
Ma,, H., Wu,, Y., Dang,, Y., Choi,, J.‐G., Zhang,, J., & Wu,, H. (2014). Pol III promoters to express small RNAs: Delineation of transcription initiation. Molecular Therapy. Nucleic Acids, 3(5), e161. https://doi.org/10.1038/mtna.2014.12
Maepa,, M. B., Ely,, A., Grayson,, W., & Arbuthnot,, P. (2017). Sustained inhibition of HBV replication in vivo after systemic injection of AAVs encoding artificial antiviral primary microRNAs. Molecular Therapy ‐ Nucleic Acids, 7, 190–199. https://doi.org/10.1016/j.omtn.2017.04.007
Maillard,, P. V., van der Veen,, A. G., Poirier,, E. Z., & Reis e Sousa,, C. (2019). Slicing and dicing viruses: Antiviral RNA interference in mammals. The EMBO Journal, 38(8). https://doi.org/10.15252/embj.2018100941
Mao,, C., Liu,, H., Chen,, P., Ye,, J., Teng,, L., Jia,, Z., & Cao,, J. (2015). Cell‐specific expression of artificial microRNAs targeting essential genes exhibit potent antitumor effect on hepatocellular carcinoma cells. Oncotarget, 6(8), 5707–5719. https://doi.org/10.18632/oncotarget.3302
Mao,, L., Liu,, S., Hu,, L., Jia,, L., Wang,, H., Guo,, M., Chen,, C., Liu,, Y., & Xu,, L. (2018). miR‐30 family: A promising regulator in development and disease. BioMed Research International, 2018. https://doi.org/10.1155/2018/9623412
Martier,, R., Liefhebber,, J. M., García‐Osta,, A., Miniarikova,, J., Cuadrado‐Tejedor,, M., Espelosin,, M., Ursua,, S., Petry,, H., van Deventer,, S. J., Evers,, M. M., & Konstantinova,, P. (2019). Targeting RNA‐mediated toxicity in C9orf72 ALS and/or FTD by RNAi‐based gene therapy. Molecular Therapy. Nucleic Acids, 16, 26–37. https://doi.org/10.1016/j.omtn.2019.02.001
Martier,, R., Liefhebber,, J. M., Miniarikova,, J., van der Zon,, T., Snapper,, J., Kolder,, I., Petry,, H., van Deventer,, S. J., Evers,, M. M., & Konstantinova,, P. (2019). Artificial MicroRNAs targeting C9orf72 can reduce accumulation of intra‐nuclear transcripts in ALS and FTD patients. Molecular Therapy. Nucleic Acids, 14, 593–608. https://doi.org/10.1016/j.omtn.2019.01.010
Martier,, R., Sogorb‐Gonzalez,, M., Stricker‐Shaver,, J., Hübener‐Schmid,, J., Keskin,, S., Klima,, J., Toonen,, L. J., Juhas,, S., Juhasova,, J., Ellederova,, Z., Motlik,, J., Haas,, E., van Deventer,, S., Konstantinova,, P., Nguyen,, H. P., & Evers,, M. M. (2019). Development of an AAV‐based microRNA gene therapy to treat Machado‐Joseph disease. Molecular Therapy ‐ Methods %26 Clinical Development, 15, 343–358. https://doi.org/10.1016/j.omtm.2019.10.008
Mashima,, R. (2015). Physiological roles of miR‐155. Immunology, 145(3), 323–333. https://doi.org/10.1111/imm.12468
McBride,, J. L., Boudreau,, R. L., Harper,, S. Q., Staber,, P. D., Monteys,, A. M., Martins,, I., Gilmore,, B. L., Burstein,, H., Peluso,, R. W., Polisky,, B., Carter,, B. J., & Davidson,, B. L. (2008). Artificial miRNAs mitigate shRNA‐mediated toxicity in the brain: Implications for the therapeutic development of RNAi. Proceedings of the National Academy of Sciences of the United States of America, 105(15), 5868–5873. https://doi.org/10.1073/pnas.0801775105
McBride,, J. L., Pitzer,, M. R., Boudreau,, R. L., Dufour,, B., Hobbs,, T., Ojeda,, S. R., & Davidson,, B. L. (2011). Preclinical safety of RNAi‐mediated HTT suppression in the rhesus macaque as a potential therapy for Huntington`s disease. Molecular Therapy, 19(12), 2152–2162. https://doi.org/10.1038/mt.2011.219
McLaughlin,, J., Cheng,, D., Singer,, O., Lukacs,, R. U., Radu,, C. G., Verma,, I. M., & Witte,, O. N. (2007). Sustained suppression of Bcr‐Abl‐driven lymphoid leukemia by microRNA mimics. Proceedings of the National Academy of Sciences of the United States of America, 104(51), 20501–20506. https://doi.org/10.1073/pnas.0710532105
McManus,, M. T., Petersen,, C. P., Haines,, B. B., Chen,, J., & Sharp,, P. A. (2002). Gene silencing using micro‐RNA designed hairpins. RNA, 8(6), 842–850.
Medley,, J. C., Panzade,, G., & Zinovyeva,, A. Y. (2020). microRNA strand selection: Unwinding the rules. WIREs RNA, e1627. https://doi.org/10.1002/wrna.1627
Michlewski,, G., & Cáceres,, J. F. (2019). Post‐transcriptional control of miRNA biogenesis. RNA, 25(1), 1–16. https://doi.org/10.1261/rna.068692.118
Miniarikova,, J., Zanella,, I., Huseinovic,, A., van der Zon,, T., Hanemaaijer,, E., Martier,, R., Koornneef,, A., Southwell,, A. L., Hayden,, M. R., van Deventer,, S. J., Petry,, H., & Konstantinova,, P. (2016). Design, characterization, and Lead selection of therapeutic miRNAs targeting Huntingtin for development of gene therapy for Huntington`s disease. Molecular Therapy. Nucleic Acids, 5, e297. https://doi.org/10.1038/mtna.2016.7
Miniarikova,, J., Zimmer,, V., Martier,, R., Brouwers,, C. C., Pythoud,, C., Richetin,, K., Rey,, M., Lubelski,, J., Evers,, M. M., van Deventer,, S. J., Petry,, H., Déglon,, N., & Konstantinova,, P. (2017). AAV5‐miHTT gene therapy demonstrates suppression of mutant huntingtin aggregation and neuronal dysfunction in a rat model of Huntington`s disease. Gene Therapy, 24(10), 630–639. https://doi.org/10.1038/gt.2017.71
Miniarikova,, J., Evers,, M. M., & Konstantinova,, P. (2018). Translation of microRNA‐based Huntingtin‐lowering therapies from preclinical studies to the clinic. Molecular Therapy: The Journal of the American Society of Gene Therapy, 26(4), 947–962. https://doi.org/10.1016/j.ymthe.2018.02.002
Monteys,, A. M., Wilson,, M. J., Boudreau,, R. L., Spengler,, R. M., & Davidson,, B. L. (2015). Artificial miRNAs targeting mutant Huntingtin show preferential silencing in vitro and in vivo. Molecular Therapy ‐ Nucleic Acids, 4, e234. https://doi.org/10.1038/mtna.2015.7
Moore,, C. B., Guthrie,, E. H., Huang,, M. T.‐H., & Taxman,, D. J. (2010). Short hairpin RNA (shRNA): Design, delivery, and assessment of gene knockdown. Methods in Molecular Biology (Clifton, N.J.), 629, 141–158. https://doi.org/10.1007/978-1-60761-657-3_10
Moore,, M. J., Scheel,, T. K. H., Luna,, J. M., Park,, C. Y., Fak,, J. J., Nishiuchi,, E., Rice,, C. M., & Darnell,, R. B. (2015). MiRNA–target chimeras reveal miRNA 3′‐end pairing as a major determinant of Argonaute target specificity. Nature Communications, 6(1), 8864. https://doi.org/10.1038/ncomms9864
Murphy,, S. R., Chang,, C. C., Dogbevia,, G., Bryleva,, E. Y., Bowen,, Z., Hasan,, M. T., & Chang,, T.‐Y. (2013). Acat1 knockdown gene therapy decreases amyloid‐β in a mouse model of Alzheimer`s disease. Molecular Therapy, 21(8), 1497–1506. https://doi.org/10.1038/mt.2013.118
NCT03282656. (2020). Clinical Trial Registration study/NCT03282656. clinicaltrials.gov. https://clinicaltrials.gov/ct2/show/study/NCT03282656
NCT04120493. (2020). Clinical Trial Registration No. NCT04120493. Available from clinicaltrials.gov. https://clinicaltrials.gov/ct2/show/NCT04120493
Neilsen,, C. T., Goodall,, G. J., & Bracken,, C. P. (2012). IsomiRs—The overlooked repertoire in the dynamic microRNAome. Trends in Genetics: TIG, 28(11), 544–549. https://doi.org/10.1016/j.tig.2012.07.005
Nguyen,, T. L., Nguyen,, T. D., Bao,, S., Li,, S., & Nguyen,, T. A. (2020). The internal loops in the lower stem of primary microRNA transcripts facilitate single cleavage of human microprocessor. Nucleic Acids Research, 48(5), 2579–2593. https://doi.org/10.1093/nar/gkaa018
Nguyen,, H. M., Nguyen,, T. D., Nguyen,, T. L., & Nguyen,, T. A. (2019). Orientation of human microprocessor on primary MicroRNAs. Biochemistry, 58(4), 189–198. https://doi.org/10.1021/acs.biochem.8b00944
Nguyen,, T. A., Jo,, M. H., Choi,, Y.‐G., Park,, J., Kwon,, S. C., Hohng,, S., Kim,, V. N., & Woo,, J.‐S. (2015). Functional anatomy of the human microprocessor. Cell, 161(6), 1374–1387. https://doi.org/10.1016/j.cell.2015.05.010
Novak,, M. J. U., & Tabrizi,, S. J. (2010). Huntington`s disease. BMJ (Clinical Research Ed.), 340, c3109. https://doi.org/10.1136/bmj.c3109
Okamura,, K., Hagen,, J. W., Duan,, H., Tyler,, D. M., & Lai,, E. C. (2007). The mirtron pathway generates microRNA‐class regulatory RNAs in drosophila. Cell, 130(1), 89–100. https://doi.org/10.1016/j.cell.2007.06.028
Olejniczak,, M., Urbanek,, M. O., Jaworska,, E., Witucki,, L., Szczesniak,, M. W., Makalowska,, I., & Krzyzosiak,, W. J. (2016). Sequence‐non‐specific effects generated by various types of RNA interference triggers. Biochimica et Biophysica Acta, 1859(2), 306–314. https://doi.org/10.1016/j.bbagrm.2015.11.005
Pan,, Y., He,, B., Chen,, J., Sun,, H., Deng,, Q., Wang,, F., Ying,, H., Liu,, X., Lin,, K., Peng,, H., Xie,, H., & Wang,, S. (2015). Gene therapy for colorectal cancer by adenovirus‐mediated siRNA targeting CD147 based on loss of the IGF2 imprinting system. International Journal of Oncology, 47(5), 1881–1889. https://doi.org/10.3892/ijo.2015.3181
Park,, J.‐E., Heo,, I., Tian,, Y., Simanshu,, D. K., Chang,, H., Jee,, D., Patel,, D. J., & Kim,, V. N. (2011). Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature, 475(7355), 201–205. https://doi.org/10.1038/nature10198
Partin,, A. C., Ngo,, T. D., Herrell,, E., Jeong,, B.‐C., Hon,, G., & Nam,, Y. (2017). Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs. Nature Communications, 8, 1737. https://doi.org/10.1038/s41467-017-01713-y
Partin,, A. C., Zhang,, K., Jeong,, B.‐C., Herrell,, E., Li,, S., Chiu,, W., & Nam,, Y. (2020). Cryo‐EM structures of human Drosha and DGCR8 in complex with primary MicroRNA. Molecular Cell, 78(3), 411–422.e4. https://doi.org/10.1016/j.molcel.2020.02.016
Paulson,, H. L. (2009). The spinocerebellar ataxias. Journal of Neuro‐Ophthalmology: The Official Journal of the North American Neuro‐Ophthalmology Society, 29(3), 227–237. https://doi.org/10.1097/WNO0b013e3181b416de
Pfister,, E. L., Chase,, K. O., Sun,, H., Kennington,, L. A., Conroy,, F., Johnson,, E., Miller,, R., Borel,, F., Aronin,, N., & Mueller,, C. (2017). Safe and efficient silencing with a pol II, but not a pol lII, promoter expressing an artificial miRNA targeting human Huntingtin. Molecular Therapy. Nucleic Acids, 7, 324–334. https://doi.org/10.1016/j.omtn.2017.04.011
Pfister,, E. L., DiNardo,, N., Mondo,, E., Borel,, F., Conroy,, F., Fraser,, C., Gernoux,, G., Han,, X., Hu,, D., Johnson,, E., Kennington,, L., Liu,, P., Reid,, S. J., Sapp,, E., Vodicka,, P., Kuchel,, T., Morton,, A. J., Howland,, D., Moser,, R., … Aronin,, N. (2018). Artificial miRNAs reduce human mutant Huntingtin throughout the striatum in a transgenic sheep model of Huntington`s disease. Human Gene Therapy, 29(6), 663–673. https://doi.org/10.1089/hum.2017.199
Ramachandran,, P. S., Bhattarai,, S., Singh,, P., Boudreau,, R. L., Thompson,, S., LaSpada,, A. R., Drack,, A. V., & Davidson,, B. L. (2014). RNA interference‐based therapy for spinocerebellar ataxia type 7 retinal degeneration. PLoS One, 9(4), e95362. https://doi.org/10.1371/journal.pone.0095362
Ramachandran,, P. S., Boudreau,, R. L., Schaefer,, K. A., La Spada,, A. R., & Davidson,, B. L. (2014). Nonallele specific silencing of ataxin‐7 improves disease phenotypes in a mouse model of SCA7. Molecular Therapy, 22(9), 1635–1642. https://doi.org/10.1038/mt.2014.108
Rao,, D. D., Vorhies,, J. S., Senzer,, N., & Nemunaitis,, J. (2009). siRNA vs. shRNA: Similarities and differences. Advanced Drug Delivery Reviews, 61(9), 746–759. https://doi.org/10.1016/j.addr.2009.04.004
Ratnavalli,, E., Brayne,, C., Dawson,, K., & Hodges,, J. R. (2002). The prevalence of frontotemporal dementia. Neurology, 58(11), 1615–1621. https://doi.org/10.1212/wnl.58.11.1615
Rayner,, K. J., Suárez,, Y., Dávalos,, A., Parathath,, S., Fitzgerald,, M. L., Tamehiro,, N., Fisher,, E. A., Moore,, K. J., & Fernández‐Hernando,, C. (2010). MiR‐33 contributes to the regulation of cholesterol homeostasis. Science (New York, N.Y.), 328(5985), 1570–1573. https://doi.org/10.1126/science.1189862
Roden,, C., Gaillard,, J., Kanoria,, S., Rennie,, W., Barish,, S., Cheng,, J., Pan,, W., Liu,, J., Cotsapas,, C., Ding,, Y., & Lu,, J. (2017). Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin‐containing transcripts and human genetic variation. Genome Research, 27(3), 374–384. https://doi.org/10.1101/gr.208900.116
Rodríguez‐Lebrón,, E., Costa,, M. d. C., Luna‐Cancalon,, K., Peron,, T. M., Fischer,, S., Boudreau,, R. L., Davidson,, B. L., & Paulson,, H. L. (2013). Silencing mutant ATXN3 expression resolves molecular phenotypes in SCA3 transgenic mice. Molecular Therapy, 21(10), 1909–1918. https://doi.org/10.1038/mt.2013.152
Ros,, X. B.‐D., & Gu,, S. (2016). Guidelines for the optimal design of miRNA‐based shRNAs. Methods (San Diego, Calif.), 103, 157–166. https://doi.org/10.1016/j.ymeth.2016.04.003
Ros,, X. B.‐D., Kasprzak,, W. K., Bhandari,, Y., Fan,, L., Cavanaugh,, Q., Jiang,, M., Dai,, L., Yang,, A., Shao,, T.‐J., Shapiro,, B. A., Wang,, Y.‐X., & Gu,, S. (2019). Structural differences between Pri‐miRNA paralogs promote alternative drosha cleavage and expand target repertoires. Cell Reports, 26(2), 447–459. https://doi.org/10.1016/j.celrep.2018.12.054
Ross,, C. A. (2002). Polyglutamine pathogenesis: Emergence of unifying mechanisms for Huntington`s disease and related disorders. Neuron, 35(5), 819–822. https://doi.org/10.1016/s0896-6273(02)00872-3
Rossi,, J. (2008). Expression strategies for short hairpin RNA interference triggers. Human Gene Therapy, 19(4), 313–317. https://doi.org/10.1089/hum.2008.026
Saha,, A., Bhagyawant,, S. S., Parida,, M., & Dash,, P. K. (2016). Vector‐delivered artificial miRNA effectively inhibited replication of Chikungunya virus. Antiviral Research, 134, 42–49. https://doi.org/10.1016/j.antiviral.2016.08.019
Samuel,, G. H., Wiley,, M. R., Badawi,, A., Adelman,, Z. N., & Myles,, K. M. (2016). Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double‐stranded RNA. Proceedings of the National Academy of Sciences of the United States of America, 113(48), 13863–13868. https://doi.org/10.1073/pnas.1600544113
Sankaran,, V. G., Menne,, T. F., Xu,, J., Akie,, T. E., Lettre,, G., Van Handel,, B., Mikkola,, H. K. A., Hirschhorn,, J. N., Cantor,, A. B., & Orkin,, S. H. (2008). Human fetal hemoglobin expression is regulated by the developmental stage‐specific repressor BCL11A. Science (New York, N.Y.), 322(5909), 1839–1842. https://doi.org/10.1126/science.1165409
Schulz,, W. (2007). Molecular biology of human cancers: An advanced student`s textbook. Springer. https://doi.org/10.1007/978-1-4020-3186-1
Schwab,, R., Ossowski,, S., Riester,, M., Warthmann,, N., & Weigel,, D. (2006). Highly specific gene silencing by artificial microRNAs in arabidopsis. The Plant Cell, 18(5), 1121–1133. https://doi.org/10.1105/tpc.105.039834
Seidel,, K., Siswanto,, S., Brunt,, E. R. P., den Dunnen,, W., Korf,, H.‐W., & Rüb,, U. (2012). Brain pathology of spinocerebellar ataxias. Acta Neuropathologica, 124(1), 1–21. https://doi.org/10.1007/s00401-012-1000-x
Shang,, R., Baek,, S. C., Kim,, K., Kim,, B., Kim,, V. N., & Lai,, E. C. (2020). Genomic clustering facilitates nuclear processing of suboptimal Pri‐miRNA loci. Molecular Cell, 78(2), 303–316.e4. https://doi.org/10.1016/j.molcel.2020.02.009
Sharma,, H., Tripathi,, A., Kumari,, B., Vrati,, S., & Banerjee,, A. (2018). Artificial microRNA‐mediated inhibition of Japanese encephalitis virus replication in neuronal cells. Nucleic Acid Therapeutics, 28(6), 357–365. https://doi.org/10.1089/nat.2018.0743
Sheng,, P., Flood,, K. A., & Xie,, M. (2020). Short hairpin RNAs for strand‐specific small interfering RNA production. Frontiers in Bioengineering and Biotechnology, 8. https://doi.org/10.3389/fbioe.2020.00940
Shin,, K.‐J., Wall,, E. A., Zavzavadjian,, J. R., Santat,, L. A., Liu,, J., Hwang,, J.‐I., Rebres,, R., Roach,, T., Seaman,, W., Simon,, M. I., & Fraser,, I. D. C. (2006). A single lentiviral vector platform for microRNA‐based conditional RNA interference and coordinated transgene expression. Proceedings of the National Academy of Sciences, 103(37), 13759–13764. https://doi.org/10.1073/pnas.0606179103
Silva,, J. M., Li,, M. Z., Chang,, K., Ge,, W., Golding,, M. C., Rickles,, R. J., Siolas,, D., Hu,, G., Paddison,, P. J., Schlabach,, M. R., Sheth,, N., Bradshaw,, J., Burchard,, J., Kulkarni,, A., Cavet,, G., Sachidanandam,, R., McCombie,, W. R., Cleary,, M. A., Elledge,, S. J., & Hannon,, G. J. (2005). Second‐generation shRNA libraries covering the mouse and human genomes. Nature Genetics, 37(11), 1281–1288. https://doi.org/10.1038/ng1650
Sittler,, A., Muriel,, M.‐P., Marinello,, M., Brice,, A., den Dunnen,, W., & Alves,, S. (2018). Deregulation of autophagy in postmortem brains of Machado‐Joseph disease patients. Neuropathology: Official Journal of the Japanese Society of Neuropathology, 38(2), 113–124. https://doi.org/10.1111/neup.12433
Sliva,, K., & Schnierle,, B. S. (2010). Selective gene silencing by viral delivery of short hairpin RNA. Virology Journal, 7. https://doi.org/10.1186/1743-422X-7-248
Son,, J., Uchil,, P. D., Kim,, Y. B., Shankar,, P., Kumar,, P., & Lee,, S.‐K. (2008). Effective suppression of HIV‐1 by artificial bispecific miRNA targeting conserved sequences with tolerance for wobble base‐pairing. Biochemical and Biophysical Research Communications, 374(2), 214–218. https://doi.org/10.1016/j.bbrc.2008.06.125
Spronck,, E. A., Brouwers,, C. C., Vallès,, A., de Haan,, M., Petry,, H., van Deventer,, S. J., Konstantinova,, P., & Evers,, M. M. (2019). AAV5‐miHTT gene therapy demonstrates sustained Huntingtin lowering and functional improvement in Huntington disease mouse models. Molecular Therapy. Methods %26 Clinical Development, 13, 334–343. https://doi.org/10.1016/j.omtm.2019.03.002
Stanek,, L. M., Sardi,, S. P., Mastis,, B., Richards,, A. R., Treleaven,, C. M., Taksir,, T., Misra,, K., Cheng,, S. H., & Shihabuddin,, L. S. (2014). Silencing mutant Huntingtin by Adeno‐associated virus‐mediated RNA interference ameliorates disease manifestations in the YAC128 mouse model of Huntington`s disease. Human Gene Therapy, 25(5), 461–474. https://doi.org/10.1089/hum.2013.200
Stegmeier,, F., Hu,, G., Rickles,, R. J., Hannon,, G. J., & Elledge,, S. J. (2005). A lentiviral microRNA‐based system for single‐copy polymerase II‐regulated RNA interference in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 102(37), 13212–13217. https://doi.org/10.1073/pnas.0506306102
Stoica,, L., Todeasa,, S. H., Cabrera,, G. T., Salameh,, J. S., ElMallah,, M. K., Mueller,, C., Brown,, R. H., & Miguel,, S.‐E. (2016). AAV delivered artificial microRNA extends survival and delays paralysis in an amyotrophic lateral sclerosis mouse model. Annals of Neurology, 79(4), 687–700. https://doi.org/10.1002/ana.24618
Sun,, B.‐S., Dong,, Q.‐Z., Ye,, Q.‐H., Sun,, H.‐J., Jia,, H.‐L., Zhu,, X.‐Q., Liu,, D.‐Y., Chen,, J., Xue,, Q., Zhou,, H.‐J., Ren,, N., & Qin,, L.‐X. (2008). Lentiviral‐mediated miRNA against osteopontin suppresses tumor growth and metastasis of human hepatocellular carcinoma. Hepatology, 48(6), 1834–1842. https://doi.org/10.1002/hep.22531
Thakral,, S., & Ghoshal,, K. (2015). MiR‐122 is a unique molecule with great potential in diagnosis, prognosis of liver disease, and therapy both as miRNA mimic and antimir. Current Gene Therapy, 15(2), 142–150.
Tiwari,, S., Atluri,, V., Kaushik,, A., Yndart,, A., & Nair,, M. (2019). Alzheimer`s disease: Pathogenesis, diagnostics, and therapeutics. International Journal of Nanomedicine, 14, 5541–5554. https://doi.org/10.2147/IJN.S200490
Van den Haute,, C., Eggermont,, K., Nuttin,, B., Debyser,, Z., & Baekelandt,, V. (2003). Lentiviral vector‐mediated delivery of short hairpin RNA results in persistent knockdown of gene expression in mouse brain. Human Gene Therapy, 14(18), 1799–1807. https://doi.org/10.1089/104303403322611809
Walder,, R. Y., Gautam,, M., Wilson,, S. P., Benson,, C. J., & Sluka,, K. A. (2011). Selective targeting of ASIC3 using artificial miRNAs inhibits primary and secondary hyperalgesia after muscle inflammation. Pain, 152(10), 2348–2356. https://doi.org/10.1016/j.pain.2011.06.027
Wallace,, L. M., Liu,, J., Domire,, J. S., Garwick‐Coppens,, S. E., Guckes,, S. M., Mendell,, J. R., Flanigan,, K. M., & Harper,, S. Q. (2012). RNA interference inhibits DUX4‐induced muscle toxicity in vivo: Implications for a targeted FSHD therapy. Molecular Therapy, 20(7), 1417–1423. https://doi.org/10.1038/mt.2012.68
Wallace,, L. M., Saad,, N. Y., Pyne,, N. K., Fowler,, A. M., Eidahl,, J. O., Domire,, J. S., Griffin,, D. A., Herman,, A. C., Sahenk,, Z., Rodino‐Klapac,, L. R., & Harper,, S. Q. (2017). Pre‐clinical safety and off‐target studies to support translation of AAV‐mediated RNAi therapy for FSHD. Molecular Therapy. Methods %26 Clinical Development, 8, 121–130. https://doi.org/10.1016/j.omtm.2017.12.005
Wang,, D., Tai,, P. W. L., & Gao,, G. (2019). Adeno‐associated virus vector as a platform for gene therapy delivery. Nature Reviews Drug Discovery, 18(5), 358–378. https://doi.org/10.1038/s41573-019-0012-9
Wang,, J., Lee,, J. E., Riemondy,, K., Yu,, Y., Marquez,, S. M., Lai,, E. C., & Yi,, R. (2020). XPO5 promotes primary miRNA processing independently of RanGTP. Nature Communications, 11(1), 1845. https://doi.org/10.1038/s41467-020-15598-x
Wang,, S., Shu,, J.‐Z., Cai,, Y., Bao,, Z., & Liang,, Q.‐M. (2012). Establishment and characterization of MTDH knockdown by artificial MicroRNA interference—Functions as a potential tumor suppressor in breast cancer. Asian Pacific Journal of Cancer Prevention: APJCP, 13(6), 2813–2818. https://doi.org/10.7314/apjcp.2012.13.6.2813
Wang,, Y., Yan,, L., Zhang,, L., Xu,, H., Chen,, T., Li,, Y., Wang,, H., Chen,, S., Wang,, W., Chen,, C., & Yang,, Q. (2018). NT21MP negatively regulates paclitaxel‐resistant cells by targeting miR‐155‐3p and miR‐155‐5p via the CXCR4 pathway in breast cancer. International Journal of Oncology, 53(3), 1043–1054. https://doi.org/10.3892/ijo.2018.4477
Wen,, J., Ladewig,, E., Shenker,, S., Mohammed,, J., & Lai,, E. C. (2015). Analysis of nearly one thousand mammalian mirtrons reveals novel features of dicer substrates. PLoS Computational Biology, 11(9), e1004441. https://doi.org/10.1371/journal.pcbi.1004441
Wu,, Z., Asokan,, A., & Samulski,, R. J. (2006). Adeno‐associated virus serotypes: Vector toolkit for human gene therapy. Molecular Therapy: The Journal of the American Society of Gene Therapy, 14(3), 316–327. https://doi.org/10.1016/j.ymthe.2006.05.009
Xia,, X.‐G., Zhou,, H., & Xu,, Z. (2006). Multiple shRNAs expressed by an inducible pol II promoter can knock down the expression of multiple target genes. BioTechniques, 41(1), 64–68. https://doi.org/10.2144/000112198
Xie,, J., Mao,, Q., Tai,, P. W. L., He,, R., Ai,, J., Su,, Q., Zhu,, Y., Ma,, H., Li,, J., Gong,, S., Wang,, D., Gao,, Z., Li,, M., Zhong,, L., Zhou,, H., & Gao,, G. (2017). Short DNA hairpins compromise recombinant adeno‐associated virus genome homogeneity. Molecular Therapy, 25(6), 1363–1374. https://doi.org/10.1016/j.ymthe.2017.03.028
Xie,, J., Tai,, P. W. L., Brown,, A., Gong,, S., Zhu,, S., Wang,, Y., Li,, C., Colpan,, C., Su,, Q., He,, R., Ma,, H., Li,, J., Ye,, H., Ko,, J., Zamore,, P. D., & Gao,, G. (2020). Effective and accurate gene silencing by a recombinant AAV‐compatible microRNA scaffold. Molecular Therapy, 28(2), 422–430. https://doi.org/10.1016/j.ymthe.2019.11.018
Xie,, M., Li,, M., Vilborg,, A., Lee,, N., Shu,, M.‐D., Yartseva,, V., Šestan,, N., & Steitz,, J. A. (2013). Mammalian 5′‐capped MicroRNA precursors that generate a single MicroRNA. Cell, 155(7), 1568–1580. https://doi.org/10.1016/j.cell.2013.11.027
Xie,, P., Xie,, Y., Zhang,, X., Huang,, H., He,, L., Wang,, X., & Wang,, S. (2013). Inhibition of dengue virus 2 replication by artificial microRNAs targeting the conserved regions. Nucleic Acid Therapeutics, 23(4), 244–252. https://doi.org/10.1089/nat.2012.0405
Yang,, J.‐S., Maurin,, T., Robine,, N., Rasmussen,, K. D., Jeffrey,, K. L., Chandwani,, R., Papapetrou,, E. P., Sadelain,, M., O`Carroll,, D., & Lai,, E. C. (2010). Conserved vertebrate mir‐451 provides a platform for Dicer‐independent, Ago2‐mediated microRNA biogenesis. Proceedings of the National Academy of Sciences, 107(34), 15163–15168. https://doi.org/10.1073/pnas.1006432107
Yang,, Y.‐S., Xie,, J., Chaugule,, S., Wang,, D., Kim,, J.‐M., Kim,, J., Tai,, P. W. L., Seo,, S., Gravallese,, E., Gao,, G., & Shim,, J.‐H. (2020). Bone‐targeting AAV‐mediated gene silencing in osteoclasts for osteoporosis therapy. Molecular Therapy ‐ Methods %26 Clinical Development, 17, 922–935. https://doi.org/10.1016/j.omtm.2020.04.010
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 %26 Development, 17(24), 3011–3016. https://doi.org/10.1101/gad.1158803
Yi,, T., Arthanari,, H., Akabayov,, B., Song,, H., Papadopoulos,, E., Qi,, H. H., Jedrychowski,, M., Güttler,, T., Guo,, C., Luna,, R. E., Gygi,, S. P., Huang,, S. A., & Wagner,, G. (2015). EIF1A augments Ago2‐mediated dicer‐independent miRNA biogenesis and RNA interference. Nature Communications, 6, 7194. https://doi.org/10.1038/ncomms8194
Yoda,, M., Cifuentes,, D., Izumi,, N., Sakaguchi,, Y., Suzuki,, T., Giraldez,, A. J., & Tomari,, Y. (2013). PARN mediates 3′‐end trimming of Argonaute2‐cleaved precursor microRNAs. Cell Reports, 5(3), 715–726. https://doi.org/10.1016/j.celrep.2013.09.029
Yu,, T., Ma,, P., Wu,, D., Shu,, Y., & Gao,, W. (2018). Functions and mechanisms of microRNA‐31 in human cancers. Biomedicine %26 Pharmacotherapy, 108, 1162–1169. https://doi.org/10.1016/j.biopha.2018.09.132
Yue,, J., Sheng,, Y., Ren,, A., & Penmatsa,, S. (2010). A miR‐21 hairpin structure‐based gene knockdown vector. Biochemical and Biophysical Research Communications, 394(3), 667–672. https://doi.org/10.1016/j.bbrc.2010.03.047
Zeng,, Y., & Cullen,, B. R. (2003). Sequence requirements for micro RNA processing and function in human cells. RNA (New York, N.Y.), 9(1), 112–123. https://doi.org/10.1261/rna.2780503
Zeng,, Y., & Cullen,, B. R. (2005). Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. The Journal of Biological Chemistry, 280(30), 27595–27603. https://doi.org/10.1074/jbc.M504714200
Zeng,, Y., Wagner,, E. J., & Cullen,, B. R. (2002). Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Molecular Cell, 9(6), 1327–1333. https://doi.org/10.1016/S1097-2765(02)00541-5
Zeng,, Y., Yi,, R., & Cullen,, B. R. (2003). MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proceedings of the National Academy of Sciences, 100(17), 9779–9784. https://doi.org/10.1073/pnas.1630797100
Zhang,, H., Kolb,, F. A., Jaskiewicz,, L., Westhof,, E., & Filipowicz,, W. (2004). Single processing center models for human dicer and bacterial RNase III. Cell, 118(1), 57–68. https://doi.org/10.1016/j.cell.2004.06.017
Zhang,, H., Tang,, X., Zhu,, C., Song,, Y., Yin,, J., Xu,, J., Ertl,, H. C. J., & Zhou,, D. (2015). Adenovirus‐mediated artificial MicroRNAs targeting matrix or nucleoprotein genes protect mice against lethal influenza virus challenge. Gene Therapy, 22(8), 653–662. https://doi.org/10.1038/gt.2015.31
Zhang,, J., Liu,, Q.‐S., & Dong,, W.‐G. (2011). Blockade of proliferation and migration of gastric cancer via targeting CDH17 with an artificial microRNA. Medical Oncology (Northwood, London, England), 28(2), 494–501. https://doi.org/10.1007/s12032-010-9489-0
Zhang,, T., Cheng,, T., Wei,, L., Cai,, Y., Yeo,, A., Han,, J., Yuan,, Y. A., Zhang,, J., & Xia,, N. (2012). Efficient inhibition of HIV‐1 replication by an artificial polycistronic miRNA construct. Virology Journal, 9, 118. https://doi.org/10.1186/1743-422X-9-118
Zhao,, Y., Samal,, E., & Srivastava,, D. (2005). Serum response factor regulates a muscle‐specific microRNA that targets Hand2 during cardiogenesis. Nature, 436(7048), 214–220. https://doi.org/10.1038/nature03817
Zheng,, Z., Wang,, P., Wang,, H., Zhang,, X., Wang,, M., Cucinotta,, F. A., & Wang,, Y. (2013). Combining heavy ion radiation and artificial microRNAs to target the homologous recombination repair gene efficiently kills human tumor cells. International Journal of Radiation Oncology, Biology, Physics, 85, 466–471. https://doi.org/10.1016/j.ijrobp.2012.04.008
Zhou,, H., Xia,, X. G., & Xu,, Z. (2005). An RNA polymerase II construct synthesizes short‐hairpin RNA with a quantitative indicator and mediates highly efficient RNAi. Nucleic Acids Research, 33(6), e62. https://doi.org/10.1093/nar/gni061
Zoghbi,, H. Y., & Orr,, H. T. (2000). Glutamine repeats and neurodegeneration. Annual Review of Neuroscience, 23, 217–247. https://doi.org/10.1146/annurev.neuro.23.1.217