Citations of papers with Morpholinos blocking miRNA activity are here.

Morpholino oligos can block the activity of microRNAs. Morpholinos complementary to the miRNA guide strand can block activity of the miRNA. Morpholinos can also block the Drosha or Dicer nucleolytic processing sites of primary miRNA or pre-miRNA. Morpholinos can interfere with miRNA activity when targeted to the miRNA's target site (MRE) on mRNA. Gene Tools assists in targeting 25-base Morpholino oligos to miRNAs, ideally using sequence information from the Sanger Institute's miRBase.

Morpholinos are usually targeted to one of these sites (shown on the lower part of figure below):

• Guide
• Star
• Guide Drosha
• Guide Dicer
• Star Drosha
• Star Dicer

Please suggest a target site when requesting design of a Morpholino targeting an miRNA. Also, specify the miRNA to target using the ID format used on the Sanger Institute's miRBase. For example, to specify Danio rerio miRNA 126b-2 write "miR-125b-2".

Note that Dicer activity is not requred for maturation of all miRNAs. Here is a known case where miRNA maturation is independent of Dicer activity:
Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science. 2010 Jun 25;328(5986):1694-8. Epub 2010 May 6.

Morpholinos can also be targeted to the site on an mRNA where a miRNA binds, called the miRNA response element (MRE). Usually these are found in the 3'-UTR of an mRNA. A Morpholino that binds across an MRE is called a target protector. To design target protector Morpholinos, we need about 60 bases of mRNA sequence centered on the MRE, written mostly in upper case but with the bases complementary to the miRNA seed sequence shown in lower case.

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References

Xu RR, Zhang CW, Cao Y, Wang Q. [mir122 deficiency inhibits differentiation of zebrafish hepatoblast into hepatocyte]. Yi Chuan. 2013 Apr;35(4):488-94. Chinese.

Kolpa HJ, Peal DS, Lynch SN, Giokas AC, Ghatak S, Misra S, Norris RA, Macrae CA, Markwald RR, Ellinor P, Bischoff J, Milan DJ. miR-21 represses Pdcd4 during cardiac valvulogenesis. Development. 2013 May;140(10):2172-80. doi: 10.1242/dev.084475. Epub 2013 Apr 11.

Avellino R, Carrella S, Pirozzi M, Risolino M, Salierno FG, Franco P, Stoppelli P, Verde P, Banfi S, Conte I. miR-204 Targeting of Ankrd13A Controls Both Mesenchymal Neural Crest and Lens Cell Migration. PLoS ONE. 2013;8(4):e61099. doi:10.1371/journal.pone.0061099

Shaham O, Gueta K, Mor E, Oren-Giladi P, Grinberg D, Xie Q, Cvekl A, Shomron N, Davis N, Keydar-Prizant M, Raviv S, Pasmanik-Chor M, Bell RE, Levy C, Avellino R, Banfi S, Conte I, Ashery-Padan R. Pax6 Regulates Gene Expression in the Vertebrate Lens through miR-204. PLoS Genet. 2013;9(3):e1003357. doi:10.1371/journal.pgen.1003357

Wei C, Thatcher EJ, Olena AF, Cha DJ, Perdigoto AL, Marshall AF, Carter BD, Broadie K, Patton JG. miR-153 Regulates SNAP-25, Synaptic Transmission, and Neuronal Development. PLoS One. 2013;8(2):e57080. doi: 10.1371/journal.pone.0057080. Epub 2013 Feb 25.

Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013 Feb 27. doi: 10.1038/nature11928. [Epub ahead of print]
Knockdown of dre-miR-7

Zhu Y, Wang D, Wang F, Li T, Dong L, Liu H, Ma Y, Jiang F, Yin H, Yan W, Luo M, Tang Z, Zhang G, Wang Q, Zhang J, Zhou J, Yu J. A comprehensive analysis of GATA-1-regulated miRNAs reveals miR-23a to be a positive modulator of erythropoiesis. Nucleic Acids Res. 2013 Feb 17. [Epub ahead of print]

Kaluza D, Kroll J, Gesierich S, Manavski Y, Boeckel JN, Doebele C, Zelent A, Rössig L, Zeiher AM, Augustin HG, Urbich C, Dimmeler S. Histone Deacetylase 9 Promotes Angiogenesis by Targeting the Antiangiogenic MicroRNA 17-92 Cluster in Endothelial Cells. Arterioscler Thromb Vasc Biol. 2013 Jan 3. [Epub ahead of print]

Chang SH, Lu YC, Li X, Hsieh WY, Xiong Y, Ghosh M, Evans T, Elemento O, Hla T. Antagonistic function of the RNA-binding protein HuR and miR-200b in post-transcriptional regulation of VEGF-A expression and angiogenesis. J Biol Chem. 2012;[Epub ahead of print]doi:10.1074/jbc.M112.423871

Lalwani MK, Sharma M, Singh AR, Chauhan RK, Patowary A, Singh N, Scaria V, Sivasubbu S. Reverse Genetics Screen in Zebrafish Identifies a Role of miR-142a-3p in Vascular Development and Integrity. PLoS ONE. 2012;7(12):e52588. doi:10.1371/journal.pone.0052588

Bridge G, Monteiro R, Henderson S, Emuss V, Lagos D, Georgopoulou D, Patient R, Boshoff C. The microRNA-30 family targets DLL4 to modulate endothelial cell behavior during angiogenesis. Blood 2012;[Epub ahead of print] doi:10.1182/blood-2012-04-423004
Target protector against the miR-30 site within the dll4 3′UTR.

Chiavacci E, Dolfi L, Verduci L, Meghini F, Gestri G, Evangelista AMM, Wilson SW, Cremisi F, Pitto L. MicroRNA 218 Mediates the Effects of Tbx5a Over-Expression on Zebrafish Heart Development. PLoS ONE. 2012;7(11):e50536. doi:10.1371/journal.pone.0050536

Stahlhut C, Suárez Y, Lu J, Mishima Y, Giraldez AJ. miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish. Development. 2012;139:4356-4365. doi:10.1242/dev.083774

Inui M, Montagner M, Ben-Zvi D, Martello G, Soligo S, Manfrin A, Aragona M, Enzo E, Zacchigna L, Zanconato F, Azzolin L, Dupont S, Cordenonsi M, Piccolo S. Self-regulation of the head-inducing properties of the Spemann organizer. Proc Natl Acad Sci U S A. 2012 Sep 4. [Epub ahead of print]
Xla-miR-15/16 Morpholinos in Xenopus laevis.

Hassel D, Cheng P, White MP, Ivey KN, Kroll J, Augustin HG, Katus HA, Stainier DY, Srivastava D. miR-10 Regulates the Angiogenic Behavior of Zebrafish and Human Endothelial Cells by Promoting VEGF Signaling. Circ Res. 2012 Sep 5. [Epub ahead of print]

Domínguez-Bendala J, Álvarez-Cubela S, Nieto M, Vargas N, Espino-Grosso P, Sacher VY, Pileggi A, García E, Ricordi C, Inverardi L, Pastori RL. Intracardial Embryonic Delivery of Developmental Modifiers In Utero. Cold Spring Harb Protoc. 2012;doi:10.1101/pdb.prot069427
Vivo-Morpholino targeting miRNA in mouse embryos.

Nishiyama T, Kaneda R, Ono T, Tohyama S, Hashimoto H, Endo J, Tsuruta H, Yuasa S, Ieda M, Makino S, Fukuda K. miR-142-3p is essential for hematopoiesis and affects cardiac cell fate in zebrafish. Biochem Biophys Res Commun. 2012 Aug 2. [Epub ahead of print]

Sessa R, Seano G, di Blasio L, Gagliardi PA, Isella C, Medico E, Cotelli F, Bussolino F, Primo L. The miR-126 regulates Angiopoietin-1 signaling and vessel maturation by targeting p85β. Biochim Biophys Acta. 2012 Jul 31. [Epub ahead of print]

Liu X, Ning G, Meng A, Wang Q. MicroRNA-206 regulates cell movements during zebrafish gastrulation by targeting prickle1a and regulating JNK2 phosphorylation. Mol Cell Biol. 2012 May 21. [Epub ahead of print]

Furlong F, Fitzpatrick P, O'Toole S, Phelan S, McGrogan B, Maguire A, O'Grady A, Gallagher M, Prencipe M, McGoldrick A, McGettigan P, Brennan D, Sheils O, Martin C, W Kay E, O'Leary J, McCann A. Low MAD2 expression levels associate with reduced progression-free survival in patients with high-grade serous epithelial ovarian cancer. J Pathol. 2012 Apr;226(5):746-55. doi: 10.1002/path.3035. Epub 2012 Jan 17.
Target protector

Biyashev D, Veliceasa D, Topczewski J, Topczewska JM, Mizgirev I, Vinokour E, Reddi AL, Licht JD, Revskoy SY, Volpert OV. miR-27b controls venous specification and tip cell fate. Blood. 2012 Mar 15;119(11):2679-87. doi: 10.1182/blood-2011-07-370635. Epub 2011 Dec 29.

Zeng L, Childs SJ. The smooth muscle microRNA miR-145 regulates gut epithelial development via a paracrine mechanism. Dev Biol. 2012;[Epub ahead of print] doi:10.1016/j.ydbio.2012.05.009.

Nicoli S, Knyphausen CP, Zhu LJ, Lakshmanan A, Lawson ND. miR-221 Is Required for Endothelial Tip Cell Behaviors during Vascular Development. Dev Cell. 2012 Feb 14;22(2):418-29.
dre-miR-221 Morpholino

Mishima Y, Fukao A, Kishimoto T, Sakamoto H, Fujiwara T, Inoue K. Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish. Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1104-9. Epub 2012 Jan 9.
dre-miR-1/206 Morpholino.

Urbich C, Kaluza D, Frömel T, Knau A, Bennewitz K, Boon RA, Bonauer A, Doebele C, Boeckel JN, Hergenreider E, Zeiher AM, Kroll J, Fleming I, Dimmeler S. MicroRNA-27a/b controls endothelial cell repulsion and angiogenesis by targeting semaphorin 6A. Blood. 2011 Dec 19. [Epub ahead of print]
miRNA knockdown in zebrafish embryos.

Tal TL, Franzosa JA, Tilton SC, Philbrick KA, Iwaniec UT, Turner RT, Waters KM, Tanguay RL. MicroRNAs control neurobehavioral development and function in zebrafish. FASEB J. 2012 Jan 17. [Epub ahead of print]

Dill H, Linder B, Fehr A, Fischer U. Intronic miR-26b controls neuronal differentiation by repressing its host transcript, ctdsp2. Genes Dev. 2012;26:25-30 doi:10.1101/gad.177774.111
Knockdown of miR-26b in zebrafish embryos.

Baudet ML, Zivraj KH, Abreu-Goodger C, Muldal A, Armisen J, Blenkiron C, Goldstein LD, Miska EA, Holt CE. miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones. Nat Neurosci. 2011 Dec 4;15(1):29-38. doi: 10.1038/nn.2979.
Electroporation in Xenopus laevis cells.

Nieto M, Hevia P, Garcia E, Klein D, Alvarez-Cubela S, Bravo-Egana V, Rosero S, Molano RD, Vargas N, Ricordi C, Pileggi A, Diez J, Domínguez-Bendala J, Pastori RL. Anti sense miR-7 impairs insulin expression in developing pancreas and in cultured pancreatic buds. Cell Transplant. 2011 Dec 20. [Epub ahead of print]

Le MTN, Shyh-Chang N, Khaw SL, Chin L, Teh C, Tay J, O'Day E, Korzh V, Yang H, Lal A, Lieberman J, Lodish HF, Lim B. Conserved Regulation of p53 Network Dosage by MicroRNA–125b Occurs through Evolving miRNA–Target Gene Pairs. PLoS Genet. 2011;7(9): e1002242. doi:10.1371/journal.pgen.1002242

Lagendijk AK, Goumans MJ, Burkhard SB, Bakkers J. MicroRNA-23 Restricts Cardiac Valve Formation by Inhibiting Has2 and Extracellular Hyaluronic Acid Production. Circ Res. 2011 Sep 2;109(6):649-57. Epub 2011 Jul 21.

He X, Yan YL, Eberhart JK, Herpin A, Wagner TU, Schartl M, Postlethwait JH. miR-196 regulates axial patterning and pectoral appendage initiation. Dev Biol. 2011 Jul 20. [Epub ahead of print]

Kapsimali M, Kaushik A-L, Gibon G, Dirian L, Ernest S, Rosa FM. Fgf signaling controls pharyngeal taste bud formation through miR-200 and Delta-Notch activity. Development. 2011;138:3473-84. doi:10.1242/dev.058669
Knockdowns of miR-200a, miR-200b and/or miR-429.

Marcet B, Chevalier B, Luxardi G, Coraux C, Zaragosi LE, Cibois M, Robbe-Sermesant K, Jolly T, Cardinaud B, Moreilhon C, Giovannini-Chami L, Nawrocki-Raby B, Birembaut P, Waldmann R, Kodjabachian L, Barbry P. Control of vertebrate multiciliogenesis by miR-449 through direct repression of the Delta/Notch pathway. Nat Cell Biol. 2011 May 22. [Epub ahead of print]
Morpholino targeting miR-499 and a Dll1 target protector.

Miyasaka KY, Kida YS, Banjo T, Ueki Y, Nagayama K, Matsumoto T, Sato M, Ogura T. Heartbeat regulates cardiogenesis by suppressing retinoic acid signaling via expression of miR-143. Mech Dev. 2011 Jan-Feb;128(1-2):18-28. Epub 2010 Sep 30.

Shieh JTC, Huang Y, Gilmore J, Srivastava D. Elevated miR-499 Levels Blunt the Cardiac Stress Response. PLoS ONE. 2011;6(5):e19481. doi:10.1371/journal.pone.0019481
Oligo targeting miR-499 electroporated into ventricular cardiomyocyte line H9c2.

Gilligan PC, Kumari P, Lim S, Cheong A, Chang A, Sampath K. Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element. Nucleic Acids Res. 2011 Apr 1;39(8):3340-9. Epub 2010 Dec 10.
Target protector

Li N, Wei C, Olena AF, Patton JG. Regulation of endoderm formation and left-right asymmetry by miR-92 during early zebrafish development. Development. 2011 May;138(9):1817-26. Epub 2011 Mar 29.

Yu YM, Gibbs KM, Davila J, Campbell N, Sung S, Todorova TI, Otsuka S, Sabaawy HE, Hart RP, Schachner M. MicroRNA miR-133b is essential for functional recovery after spinal cord injury in adult zebrafish. Eur J Neurosci. 2011 May;33(9):1587-97. doi: 10.1111/j.1460-9568.2011.07643.x. Epub 2011 Mar 30.
Morpholino solution soaked on Gelfoam and applied to lesion.

Fish JE, Wythe JD, Xiao T, Bruneau BG, Stainier DY, Srivastava D, Woo S. A Slit/miR-218/Robo regulatory loop is required during heart tube formation in zebrafish. Development. 2011 Apr;138(7):1409-19.

Hwang-Verslues WW, Chang PH, Wei PC, Yang CY, Huang CK, Kuo WH, Shew JY, Chang KJ, Lee EY, Lee WH. miR-495 is upregulated by E12/E47 in breast cancer stem cells, and promotes oncogenesis and hypoxia resistance via downregulation of E-cadherin and REDD1. Oncogene. 2011 Jan 24. [Epub ahead of print]

Staton AA, Knaut H, Giraldez AJ. miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration. Nat Genet. 2011 Jan 23. [Epub ahead of print]
Target protectors

Bonev B, Pisco A, Papalopulu N. MicroRNA-9 Reveals Regional Diversity of Neural Progenitors along the Anterior-Posterior Axis. Dev Cell. 2011 Jan 18;20(1):19-32.
Targeting Xtr-miR-9 and target protecting hairy1.

Zou J, Li WQ, Li Q, Li XQ, Zhang JT, Liu GQ, Chen J, Qiu XX, Tian FJ, Wang ZZ, Zhu N, Qin YW, Shen B, Liu TX, Jing Q. Two Functional MicroRNA-126s Repress a Novel Target Gene p21-Activated Kinase 1 to Regulate Vascular Integrity in Zebrafish. Circ Res. 2010 Dec 9. [Epub ahead of print]

Ghosh G, Subramanian IV, Adhikari N, Zhang X, Joshi HP, Basi D, Chandrashekhar YS, Hall JL, Roy S, Zeng Y, Ramakrishnan S. Hypoxia-induced microRNA-424 expression in human endothelial cells regulates HIF-α isoforms and promotes angiogenesis. J Clin Invest. 2010 Oct 25. pii: 42980. doi: 10.1172/JCI42980. [Epub ahead of print]

Conte I, Carrella S, Avellino R, Karali M, Marco-Ferreres R, Bovolenta P, Banfi S. miR-204 is required for lens and retinal development via Meis2 targeting. Proc Natl Acad Sci U S A. 2010 Aug 16. [Epub ahead of print]

Yu D, dos Santos CO, Zhao G, Jiang J, Amigo JD, Khandros E, Dore LC, Yao Y, D'Souza J, Zhang Z, Ghaffari S, Choi J, Friend S, Tong W, Orange JS, Paw BH, Weiss MJ. miR-451 protects against erythroid oxidant stress by repressing 14-3-3zeta. Genes Dev. 2010 Aug 1;24(15):1620-33.

Pedrioli DM, Karpanen T, Dabouras V, Jurisic G, van de Hoek G, Shin JW, Marino D, Kälin RE, Leidel S, Cinelli P, Schulte-Merker S, Brändli AW, Detmar M. miR-31 functions as a negative regulator of lymphatic vascular lineage-specific differentiation in vitro and vascular development in vivo. Mol Cell Biol. 2010 Jul;30(14):3620-34. Epub 2010 May 17.

Deacon DC, Nevis KR, Cashman TJ, Zhou Y, Zhao L, Washko D, Guner-Ataman B, Burns CG, Burns CE. The miR-143-adducin3 pathway is essential for cardiac chamber morphogenesis. Development. 2010 Jun;137(11):1887-96.
See supplemental online information for comparison figure of various Morpholino oligos targeting dre-miR-143 on guide or star strands.

Long J, Wang Y, Wang W, Chang BH, Danesh FR. Identification of MicroRNA-93 as a novel regulator of vascular endothelial growth factor (VEGF) in hyperglycemic conditions. J Biol Chem. 2010 May 25. [Epub ahead of print]
Delivery note: abstract mentions peptide-conjugated Morpholino oligomers, but mat'l and methods describes Endo-Porter.

Nicoli S, Standley C, Walker P, Hurlstone A, Fogarty KE, Lawson ND. MicroRNA-mediated integration of haemodynamics and Vegf signalling during angiogenesis. Nature. 2010 Apr 4. [Epub ahead of print]

Hsu RJ, Lin CY, Hoi HS, Zheng SK, Lin CC, Tsai HJ. Novel intronic microRNA represses zebrafish myf5 promoter activity through silencing dickkopf-3 gene. Nucleic Acids Res. 2010 Mar 17. [Epub ahead of print]

Zhao X, He X, Han X, Yu Y, Ye F, Chen Y, Hoang T, Xu X, Mi QS, Xin M, Wang F, Appel B, Lu QR. MicroRNA-Mediated Control of Oligodendrocyte Differentiation. Neuron. 2010 Mar 11;65(5):612-626.

Li H, Kloosterman W, Fekete DM. MicroRNA-183 Family Members Regulate Sensorineural Fates in the Inner Ear. J Neurosci. 2010 Mar 3;30(9):3254-63.

Hu H, Du L, Nagabayashi G, Seeger RC, Gatti RA. ATM is down-regulated by N-Myc-regulated microRNA-421. Proc Natl Acad Sci U S A. 2010 Jan 4. [Epub ahead of print]

Sheedy FJ, Palsson-McDermott E, Hennessy EJ, Martin C, O'Leary J, Ruan Q, Johnson DP, Chen Y, O'Neill LA. Negative regulation of TLR4 via targeting of the proinflammatory tumor suppressor PDCD4 by the microRNA miR-21. Nat Immunol. 2009 Nov 29. [Epub ahead of print]
NOTE: Target protector for miR-21

Agrawal R, Tran U, Wessely O. The miR-30 miRNA family regulates Xenopus pronephros development and targets the transcription factor Xlim1/Lhx1. Development. 2009 Dec;136(23):3927-36.

Zeng L, Carter AD, Childs SJ. miR-145 directs intestinal maturation in zebrafish. Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17793-8. Epub 2009 Oct 5.

Weiss FU, Marques IJ, Woltering JM, Vlecken DH, Aghdassi A, Partecke LI, Heidecke CD, Lerch MM, Bagowski CP. Retinoic acid receptor (RAR) antagonists inhibit miR-10a expression and block metastatic behaviour of pancreatic cancer. Gastroenterology. 2009 Sep 9. [Epub ahead of print]

Lin Z, Murtaza I, Wang K, Jiao J, Gao J, Li PF. miR-23a functions downstream of NFATc3 to regulate cardiac hypertrophy. Proc Natl Acad Sci U S A. 2009 Jul 2. [Epub ahead of print]
NOTE: target protector strategy used

Walker JC, Harland RM. microRNA-24a is required to repress apoptosis in the developing neural retina. Genes Dev. 2009 May 1;23(9):1046-51. Epub 2009 Apr 16.

Le MT, Teh C, Shyh-Chang N, Xie H, Zhou B, Korzh V, Lodish HF, Lim B. MicroRNA-125b is a novel negative regulator of p53. Genes Dev. 2009 Apr 1;23(7):862-76. Epub 2009 Mar 17.

Flynt AS, Thatcher EJ, Burkewitz K, Li N, Liu Y, Patton JG. miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos. J Cell Biol. 2009 Mar 30. [Epub ahead of print]

Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev. 2009 Feb 24. [Epub ahead of print]

Du TT, Fu YF, Dong M, Wang L, Fan HB, Chen Y, Jin Y, Chen SJ, Chen Z, Deng M, Huang QH, Liu TX. Experimental validation and complexity of miRNA-mRNA target interaction during zebrafish primitive erythropoiesis. Biochem Biophys Res Commun. 2009 Apr 17;381(4):688-93. Epub 2009 Feb 28.

Thatcher EJ, Paydar I, Anderson KK, Patton JG. Regulation of zebrafish fin regeneration by microRNAs. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18384-9. Epub 2008 Nov 17.
NOTE: Electroporation of Morpholinos into fins

Zhang MC, Lv Y, Qi YT, Zhang Z, Fu XN, Yuan CG, Lai LH. [Knockdown and overexpression of miR-219 lead to embryonic defects in zebrafish development] Fen Zi Xi Bao Sheng Wu Xue Bao. 2008 Oct;41(5):341-8. Chinese.

Pase L, Layton JE, Kloosterman WP, Carradice D, Waterhouse PM, Lieschke GJ. miR-451 regulates zebrafish erythroid maturation in vivo via its target gata2. Blood. 2008 Oct 10. [Epub ahead of print]

Fish JE, Santoro MM, Morton SU, Yu S, Yeh RF, Wythe JD, Ivey KN, Bruneau BG, Stainier DY, Srivastava D. miR-126 regulates angiogenic signaling and vascular integrity. Dev Cell. 2008 Aug;15(2):272-84.

Li N, Flynt AS, Kim HR, Solnica-Krezel L, Patton JG. Dispatched Homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites. Nucleic Acids Res. 2008 Jun 26. [Epub ahead of print]
NOTE: target protector strategy used

Leucht C, Stigloher C, Wizenmann A, Klafke R, Folchert A, Bally-Cuif L. MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary. Nat Neurosci. 2008 Jun;11(6):641-648. Epub 2008 May 4.

Yin VP, Thomson JM, Thummel R, Hyde DR, Hammond SM, Poss KD. Fgf-dependent depletion of microRNA-133 promotes appendage regeneration in zebrafish. Genes Dev. 2008 Mar 15;22(6):728-33.
NOTE: Electroporation of Morpholinos into fins

Dore LC, Amigo JD, Dos Santos CO, Zhang Z, Gai X, Tobias JW, Yu D, Klein AM, Dorman C, Wu W, Hardison RC, Paw BH, Weiss MJ. A GATA-1-regulated microRNA locus essential for erythropoiesis. Proc Natl Acad Sci U S A. 2008 Feb 26; [Epub ahead of print]

Eberhart JK, He X, Swartz ME, Yan YL, Song H, Boling TC, Kunerth AK, Walker MB, Kimmel CB, Postlethwait JH. MicroRNA Mirn140 modulates Pdgf signaling during palatogenesis. Nat Genet. 2008 Feb 10; [Epub ahead of print]

Choi PS, Zakhary L, Choi WY, Caron S, Alvarez-Saavedra E, Miska EA, McManus M, Harfe B, Giraldez AJ, Horvitz RH, Schier AF, Dulac C. Members of the miRNA-200 family regulate olfactory neurogenesis. Neuron. 2008 Jan 10;57(1):41-55.

Woltering JM, Durston AJ. MiR-10 represses HoxB1a and HoxB3a in zebrafish. PLoS ONE. 2008 Jan 2;3(1):e1396.

Lin YC, Hsieh LC, Kuo MW, Yu J, Kuo HH, Lo WL, Lin RJ, Yu AL, Li WH. Human TRIM71 and Its Nematode Homologue are Targets of let-7 MicroRNA and Its Zebrafish Orthologue is Essential for Development. Mol Biol Evol. 2007 Sep 21; [Epub ahead of print]

An miRNA's target site on an mRNA can be protected by a complementary Morpholino oligo.
Choi WY, Giraldez AJ, Schier AF. Target Protectors Reveal Dampening and Balancing of Nodal Agonist and Antagonist by miR-430. Science. 2007 Oct 12;318(5848):271-4. Epub 2007 Aug 30.

Martello G, Zacchigna L, Inui M, Montagner M, Adorno M, Mamidi A, Morsut L, Soligo S, Tran U, Dupont S, Cordenonsi M, Wessely O & Piccolo S. MicroRNA control of Nodal signalling. Nature 2007 Sep 13;449(7159):183-8. Epub 2007 Aug 29

A collaboration with Wigard Kloosterman, first of Ronald Plasterk's lab then Rene Ketting's lab at the Hubrecht Institute in the Netherlands, has shown that Morpholino oligos can strongly inhibit the activity of miRNAs in zebrafish and block their detection by in-situ hybridization and Northern blots. Knockdowns of miRNA activity have generally used oligos targeting the miRNA guide strand. A Morpholino oligo targeting an miRNA guide strand can interfere with the activity of the miRNA. It is difficult to control for the specificity of the knockdown when using this technique alone. However, Morpholinos targeting the nucleolytic processing sites of an immature miRNA can prevent maturation of the miRNA. This allows sets of nonoverlapping Morpholino oligos targeting a primary miRNA to be used as specificity controls; if two non-overlapping oligos targeting the same miRNA produce the same phenotype, this supports the hypothesis that the phenotype is due to knocking down the activity of the targeted miRNA and not due to an off-target effect. These techniques are explored in the following paper:
Kloosterman WP, Lagendijk AK, Ketting RF, Moulton JD, Plasterk RHA. Targeted inhibition of miRNA maturation with morpholinos reveals a role for miR-375 in pancreatic islet development. PLoS Biol. 2007;5(8): e203.

This is the first published report we've found of data from miRNA knockdown using Morpholinos.
Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, Patton JG. Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nature Genetics 2007; 39: 259 - 263.

The following paper primarily reports experiments with 2'-O-methyl oligos but the authors also report that Morpholinos are effective in this application, though no data for the Morpholino knockdowns is shown.
Kloosterman WP, Wienholds E, Ketting RF, Plasterk RH. Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res. 2004 Dec 07;32(21):6284-91.