Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
Science Careers Booklet

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Published Online May 26, 2005
Science DOI: 10.1126/science.1114519

Reports

Submitted on May 6, 2005
Accepted on May 13, 2005

MicroRNA Expression in Zebrafish Embryonic Development

Erno Wienholds 1, Wigard P. Kloosterman 1, Eric Miska 2, Ezequiel Alvarez-Saavedra 3, Eugene Berezikov 1, Ewart de Bruijn 1, Robert H. Horvitz 3, Sakari Kauppinen 4, Ronald H. A. Plasterk 1*

1 Hubrecht Laboratory, Centre for Biomedical Genetics, Utrecht, the Netherlands.
2 Howard Hughes Medical Institute, Department of Biology and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.
3 Howard Hughes Medical Institute, Department of Biology and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA.
4 Wilhelm Johannsen Centre for Functional Genome Research, Institute of Medical Biochemistry and Genetics, University of Copenhagen, Denmark.

* To whom correspondence should be addressed.
Ronald H. A. Plasterk , E-mail: plasterk{at}niob.knaw.nl

MicroRNAs (miRNAs) are small noncoding RNAs, approximately 21 nucleotides in length, that can regulate gene expression by base-pairing to partially complementary mRNAs. Regulation by miRNAs can play essential roles in embryonic development. We determined the temporal and spatial expression patterns of 115 conserved vertebrate miRNAs in zebrafish embryos by microarrays and by in situ hybridizations, using locked-nucleic-acid-modified oligonucleotide probes. Most miRNAs were expressed in a highly tissue-specific manner during segmentation and later stages, but not early in development, suggesting that their role is not in tissue fate establishment but in differentiation or maintenance of tissue identity. Bg.g.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Dispatched Homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites.
N. Li, A. S. Flynt, H. R. Kim, L. Solnica-Krezel, and J. G. Patton (2008)
Nucleic Acids Res. 36, 4277-4285
   Abstract »    Full Text »    PDF »
Control of cardiac excitability by microRNAs.
B. Yang, Y. Lu, and Z. Wang (2008)
Cardiovasc Res
   Abstract »    Full Text »    PDF »
Inducible expression of microRNA-194 is regulated by HNF-1{alpha} during intestinal epithelial cell differentiation.
K. Hino, K. Tsuchiya, T. Fukao, K. Kiga, R. Okamoto, T. Kanai, and M. Watanabe (2008)
RNA 14, 1433-1442
   Abstract »    Full Text »    PDF »
Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis.
N. S. Sokol, P. Xu, Y.-N. Jan, and V. Ambros (2008)
Genes & Dev. 22, 1591-1596
   Abstract »    Full Text »    PDF »
Conservation of small RNA pathways in platypus.
E. P. Murchison, P. Kheradpour, R. Sachidanandam, C. Smith, E. Hodges, Z. Xuan, M. Kellis, F. Grutzner, A. Stark, and G. J. Hannon (2008)
Genome Res. 18, 995-1004
   Abstract »    Full Text »    PDF »
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach.
E. A. Glazov, P. A. Cottee, W. C. Barris, R. J. Moore, B. P. Dalrymple, and M. L. Tizard (2008)
Genome Res. 18, 957-964
   Abstract »    Full Text »    PDF »
The miR-200 Family Inhibits Epithelial-Mesenchymal Transition and Cancer Cell Migration by Direct Targeting of E-cadherin Transcriptional Repressors ZEB1 and ZEB2.
M. Korpal, E. S. Lee, G. Hu, and Y. Kang (2008)
J. Biol. Chem. 283, 14910-14914
   Abstract »    Full Text »    PDF »
RNAs as extracellular signaling molecules.
M. E Dinger, T. R Mercer, and J. S Mattick (2008)
J. Mol. Endocrinol. 40, 151-159
   Abstract »    Full Text »    PDF »
Alterations in Micro-Ribonucleic Acid Expression Profiles Reveal a Novel Pathway for Estrogen Regulation.
A. Cohen, M. Shmoish, L. Levi, U. Cheruti, B. Levavi-Sivan, and E. Lubzens (2008)
Endocrinology 149, 1687-1696
   Abstract »    Full Text »    PDF »
Gene Regulation by Transcription Factors and MicroRNAs.
O. Hobert (2008)
Science 319, 1785-1786
   Abstract »    Full Text »    PDF »
Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver.
J. Elmen, M. Lindow, A. Silahtaroglu, M. Bak, M. Christensen, A. Lind-Thomsen, M. Hedtjarn, J. B. Hansen, H. F. Hansen, E. M. Straarup, et al. (2008)
Nucleic Acids Res. 36, 1153-1162
   Abstract »    Full Text »    PDF »
Micromanaging regeneration.
E. M. Tanaka and G. Weidinger (2008)
Genes & Dev. 22, 700-705
   Full Text »    PDF »
MicroRNAs Control Gene Expression: Importance for Cardiac Development and Pathophysiology.
D. CATALUCCI, M. V. G. LATRONICO, and G. CONDORELLI (2008)
Ann. N.Y. Acad. Sci. 1123, 20-29
   Abstract »    Full Text »    PDF »
MicroRNA expression in the adult mouse central nervous system.
M. Bak, A. Silahtaroglu, M. Moller, M. Christensen, M. F. Rath, B. Skryabin, N. Tommerup, and S. Kauppinen (2008)
RNA 14, 432-444
   Abstract »    Full Text »    PDF »
MicroRNAs and the advent of vertebrate morphological complexity.
A. M. Heimberg, L. F. Sempere, V. N. Moy, P. C. J. Donoghue, and K. J. Peterson (2008)
PNAS 105, 2946-2950
   Abstract »    Full Text »    PDF »
Dicer-dependent pathways regulate chondrocyte proliferation and differentiation.
T. Kobayashi, J. Lu, B. S. Cobb, S. J. Rodda, A. P. McMahon, E. Schipani, M. Merkenschlager, and H. M. Kronenberg (2008)
PNAS 105, 1949-1954
   Abstract »    Full Text »    PDF »
Development of a Dual-Luciferase Reporter System for In Vivo Visualization of MicroRNA Biogenesis and Posttranscriptional Regulation.
J. Y. Lee, S. Kim, D. W. Hwang, J. M. Jeong, J.-K. Chung, M. C. Lee, and D. S. Lee (2008)
J. Nucl. Med. 49, 285-294
   Abstract »    Full Text »    PDF »
Asymmetric Involution of the Myocardial Field Drives Heart Tube Formation in Zebrafish.
S. Rohr, C. Otten, and S. Abdelilah-Seyfried (2008)
Circ. Res. 102, e12-e19
   Abstract »    Full Text »    PDF »
Altered MicroRNA Expression Confined to Specific Epithelial Cell Subpopulations in Breast Cancer.
L. F. Sempere, M. Christensen, A. Silahtaroglu, M. Bak, C. V. Heath, G. Schwartz, W. Wells, S. Kauppinen, and C. N. Cole (2007)
Cancer Res. 67, 11612-11620
   Abstract »    Full Text »    PDF »
Emerging Role of MicroRNAs in Cardiovascular Biology.
M. V.G. Latronico, D. Catalucci, and G. Condorelli (2007)
Circ. Res. 101, 1225-1236
   Abstract »    Full Text »    PDF »
MicroRNA-21 Knockdown Disrupts Glioma Growth In vivo and Displays Synergistic Cytotoxicity with Neural Precursor Cell Delivered S-TRAIL in Human Gliomas.
M. F. Corsten, R. Miranda, R. Kasmieh, A. M. Krichevsky, R. Weissleder, and K. Shah (2007)
Cancer Res. 67, 8994-9000
   Abstract »    Full Text »    PDF »
A simple array platform for microRNA analysis and its application in mouse tissues.
X. Tang, J. Gal, X. Zhuang, W. Wang, H. Zhu, and G. Tang (2007)
RNA 13, 1803-1822
   Abstract »    Full Text »    PDF »
MicroRNA (miRNA) Transcriptome of Mouse Retina and Identification of a Sensory Organ-specific miRNA Cluster.
S. Xu, P. D. Witmer, S. Lumayag, B. Kovacs, and D. Valle (2007)
J. Biol. Chem. 282, 25053-25066
   Abstract »    Full Text »    PDF »
MicroRNAs in the Human Heart: A Clue to Fetal Gene Reprogramming in Heart Failure.
T. Thum, P. Galuppo, C. Wolf, J. Fiedler, S. Kneitz, L. W. van Laake, P. A. Doevendans, C. L. Mummery, J. Borlak, A. Haverich, et al. (2007)
Circulation 116, 258-267
   Abstract »    Full Text »    PDF »
Role of Dicer and Drosha for Endothelial MicroRNA Expression and Angiogenesis.
A. Kuehbacher, C. Urbich, A. M. Zeiher, and S. Dimmeler (2007)
Circ. Res. 101, 59-68
   Abstract »    Full Text »    PDF »
Noncoding RNAs and RNA Editing in Brain Development, Functional Diversification, and Neurological Disease.
M. F. Mehler and J. S. Mattick (2007)
Physiol Rev 87, 799-823
   Abstract »    Full Text »    PDF »
Gallus Expression In Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database.
P. B. Antin, S. Kaur, S. Stanislaw, S. Davey, J. H. Konieczka, T. A. Yatskievych, and D. K. Darnell (2007)
Poult. Sci. 86, 1472-1477
   Abstract »    Full Text »    PDF »
A new paradigm for developmental biology.
J. S. Mattick (2007)
J. Exp. Biol. 210, 1526-1547
   Abstract »    Full Text »    PDF »
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.
H. Kikuta, M. Laplante, P. Navratilova, A. Z. Komisarczuk, P. G. Engstrom, D. Fredman, A. Akalin, M. Caccamo, I. Sealy, K. Howe, et al. (2007)
Genome Res. 17, 545-555
   Abstract »    Full Text »    PDF »
Dicer Dependent MicroRNAs Regulate Gene Expression and Functions in Human Endothelial Cells.
Y. Suarez, C. Fernandez-Hernando, J. S. Pober, and W. C. Sessa (2007)
Circ. Res. 100, 1164-1173
   Abstract »    Full Text »    PDF »
miRNAs in cancer: approaches, aetiology, diagnostics and therapy.
C. Blenkiron and E. A. Miska (2007)
Hum. Mol. Genet. 16, R106-R113
   Abstract »    Full Text »    PDF »
Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues.
L. L. Coutinho, L. K. Matukumalli, T. S. Sonstegard, C. P. Van Tassell, L. C. Gasbarre, A. V. Capuco, and T. P. L. Smith (2007)
Physiol Genomics 29, 35-43
   Abstract »    Full Text »    PDF »
Identification and Characterization of MicroRNAs Expressed in the Mouse Eye.
M. Karali, I. Peluso, V. Marigo, and S. Banfi (2007)
Invest. Ophthalmol. Vis. Sci. 48, 509-515
   Abstract »    Full Text »    PDF »
Post-transcriptional regulation of the let-7 microRNA during neural cell specification.
F. G. Wulczyn, L. Smirnova, A. Rybak, C. Brandt, E. Kwidzinski, O. Ninnemann, M. Strehle, A. Seiler, S. Schumacher, and R. Nitsch (2007)
FASEB J 21, 415-426
   Abstract »    Full Text »    PDF »
Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos.
Z. Yu, Z. Jian, S.-H. Shen, E. Purisima, and E. Wang (2007)
Nucleic Acids Res. 35, 152-164
   Abstract »    Full Text »    PDF »
MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development.
P. L. Boutz, G. Chawla, P. Stoilov, and D. L. Black (2007)
Genes & Dev. 21, 71-84
   Abstract »    Full Text »    PDF »
MicroRNAs: regulators of gene expression and cell differentiation.
R. A. Shivdasani (2006)
Blood 108, 3646-3653
   Abstract »    Full Text »    PDF »
MIR-206 regulates connexin43 expression during skeletal muscle development.
C. Anderson, H. Catoe, and R. Werner (2006)
Nucleic Acids Res. 34, 5863-5871
   Abstract »    Full Text »    PDF »
Denoising feedback loops by thresholding--a new role for microRNAs..
S. M. Cohen, J. Brennecke, and A. Stark (2006)
Genes & Dev. 20, 2769-2772
   Full Text »    PDF »
Optimization of Feline Immunodeficiency Virus Vectors for RNA Interference.
S. Q. Harper, P. D. Staber, C. R. Beck, S. K. Fineberg, C. Stein, D. Ochoa, and B. L. Davidson (2006)
J. Virol. 80, 9371-9380
   Abstract »    Full Text »    PDF »
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis.
E. Berezikov, G. van Tetering, M. Verheul, J. van de Belt, L. van Laake, J. Vos, R. Verloop, M. van de Wetering, V. Guryev, S. Takada, et al. (2006)
Genome Res. 16, 1289-1298
   Abstract »    Full Text »    PDF »
Genomic evolution of Hox gene clusters..
D. Lemons and W. McGinnis (2006)
Science 313, 1918-1922
   Abstract »    Full Text »    PDF »
From the Cover: Differences in vertebrate microRNA expression.
B. Ason, D. K. Darnell, B. Wittbrodt, E. Berezikov, W. P. Kloosterman, J. Wittbrodt, P. B. Antin, and R. H. A. Plasterk (2006)
PNAS 103, 14385-14389
   Abstract »    Full Text »    PDF »
A microRNA detection system based on padlock probes and rolling circle amplification.
S. P. Jonstrup, J. Koch, and J. Kjems (2006)
RNA 12, 1747-1752
   Abstract »    Full Text »    PDF »
Muscle-specific microRNA miR-206 promotes muscle differentiation.
H. K. Kim, Y. S. Lee, U. Sivaprasad, A. Malhotra, and A. Dutta (2006)
J. Cell Biol. 174, 677-687
   Abstract »    Full Text »    PDF »
Extensive post-transcriptional regulation of microRNAs and its implications for cancer.
J. M. Thomson, M. Newman, J. S. Parker, E. M. Morin-Kensicki, T. Wright, and S. M. Hammond (2006)
Genes & Dev. 20, 2202-2207
   Abstract »    Full Text »    PDF »
Improved In Situ Hybridization Efficiency with Locked-Nucleic-Acid-Incorporated DNA Probes.
K. Kubota, A. Ohashi, H. Imachi, and H. Harada (2006)
Appl. Envir. Microbiol. 72, 5311-5317
   Abstract »    Full Text »    PDF »
Myogenic factors that regulate expression of muscle-specific microRNAs.
P. K. Rao, R. M. Kumar, M. Farkhondeh, S. Baskerville, and H. F. Lodish (2006)
PNAS 103, 8721-8726
   Abstract »    Full Text »    PDF »
Post-transcriptional small RNA pathways in plants: mechanisms and regulations..
H. Vaucheret (2006)
Genes & Dev. 20, 759-771
   Abstract »    Full Text »    PDF »
Reciprocal actions of REST and a microRNA promote neuronal identity.
C. Conaco, S. Otto, J.-J. Han, and G. Mandel (2006)
PNAS 103, 2422-2427
   Abstract »    Full Text »    PDF »
RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain.
P. T. NELSON, D. A. BALDWIN, W. P. KLOOSTERMAN, S. KAUPPINEN, R. H.A. PLASTERK, and Z. MOURELATOS (2006)
RNA 12, 187-191
   Abstract »    Full Text »    PDF »
Rapid Alteration of MicroRNA Levels by Histone Deacetylase Inhibition.
G. K. Scott, M. D. Mattie, C. E. Berger, S. C. Benz, and C. C. Benz (2006)
Cancer Res. 66, 1277-1281
   Abstract »    Full Text »    PDF »
The expression profile of microRNAs in mouse embryos..
J. Mineno, S. Okamoto, T. Ando, M. Sato, H. Chono, H. Izu, M. Takayama, K. Asada, O. Mirochnitchenko, M. Inouye, et al. (2006)
Nucleic Acids Res. 34, 1765-1771
   Abstract »    Full Text »    PDF »
Cloning and expression of new microRNAs from zebrafish..
W. P. Kloosterman, F. A. Steiner, E. Berezikov, E. de Bruijn, J. van de Belt, M. Verheul, E. Cuppen, and R. H.A. Plasterk (2006)
Nucleic Acids Res. 34, 2558-2569
   Abstract »    Full Text »    PDF »
The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution.
K. K.-H. Farh, A. Grimson, C. Jan, B. P. Lewis, W. K. Johnston, L. P. Lim, C. B. Burge, and D. P. Bartel (2005)
Science 310, 1817-1821
   Abstract »    Full Text »    PDF »
A novel C. elegans zinc finger transcription factor, lsy-2, required for the cell type-specific expression of the lsy-6 microRNA.
R. J. Johnston Jr and O. Hobert (2005)
Development 132, 5451-5460
   Abstract »    Full Text »    PDF »
Physiological genomics in PG and beyond: October to December 2005.
M. Liang and B. Ventura (2005)
Physiol Genomics 24, 1-3
   Full Text »    PDF »
Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development.
A. A. Aboobaker, P. Tomancak, N. Patel, G. M. Rubin, and E. C. Lai (2005)
PNAS 102, 18017-18022
   Abstract »    Full Text »    PDF »
Dramatically improved RNA in situ hybridization signals using LNA-modified probes.
R. THOMSEN, P. S. NIELSEN, and T. H. JENSEN (2005)
RNA 11, 1745-1748
   Abstract »    Full Text »    PDF »
microPrimer: the biogenesis and function of microRNA.
T. Du and P. D. Zamore (2005)
Development 132, 4645-4652
   Abstract »    Full Text »    PDF »
MicroRNA functions in animal development and human disease.
I. Alvarez-Garcia and E. A. Miska (2005)
Development 132, 4653-4662
   Abstract »    Full Text »    PDF »
Camels and zebrafish, viruses and cancer: a microRNA update.
E. Berezikov and R. H.A. Plasterk (2005)
Hum. Mol. Genet. 14, R183-R190
   Abstract »    Full Text »    PDF »
Not miR-ly muscular: microRNAs and muscle development.
J. Brennecke, A. Stark, and S. M. Cohen (2005)
Genes & Dev. 19, 2261-2264
   Full Text »    PDF »
Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth.
N. S. Sokol and V. Ambros (2005)
Genes & Dev. 19, 2343-2354
   Abstract »    Full Text »    PDF »


ADVERTISEMENT
Click Me!

ADVERTISEMENT
Click Me!

To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)