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In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes

Abstract

MicroRNAs (miRNAs) are 20–23 nucleotide (nt) RNA molecules that regulate gene expression post-transcriptionally. A key step toward understanding the function of the hundreds of miRNAs identified in animals is to determine their expression during development. Here we performed a detailed analysis of conditions for in situ detection of miRNAs in the zebrafish embryo using locked nucleic acid (LNA)-modified DNA probes and report expression patterns for 15 miRNAs in the mouse embryo.

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Figure 1: miRNA detection in zebrafish embryos using LNA-modified DNA probes.
Figure 2: Expression of 15 miRNAs in 9.5- and 10.5-d.p.c. mouse embryos.

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References

  1. Griffiths-Jones, S. Nucleic Acids Res. 32, D109–D111 (2004).

    Article  CAS  Google Scholar 

  2. Bentwich, I. et al. Nat. Genet. 37, 766–770 (2005).

    Article  CAS  Google Scholar 

  3. Berezikov, E. et al. Cell 120, 21–24 (2005).

    Article  CAS  Google Scholar 

  4. Wienholds, E. & Plasterk, R.H. FEBS Lett. 579, 5911–5922 (2005).

    Article  CAS  Google Scholar 

  5. Giraldez, A.J. et al. Science 308, 833–838 (2005).

    Article  CAS  Google Scholar 

  6. Zhao, Y., Samal, E. & Srivastava, D. Nature 436, 214–220 (2005).

    Article  CAS  Google Scholar 

  7. Lu, J. et al. Nature 435, 834–838 (2005).

    Article  CAS  Google Scholar 

  8. Wienholds, E. et al. Science 309, 310–311 (2005).

    Article  CAS  Google Scholar 

  9. Vester, B. & Wengel, J. Biochemistry 43, 13233–13241 (2004).

    Article  CAS  Google Scholar 

  10. Mansfield, J.H. et al. Nat. Genet. 36, 1079–1083 (2004).

    Article  CAS  Google Scholar 

  11. Sempere, L.F. et al. Genome Biol. 5, R13 (2004).

    Article  Google Scholar 

  12. Thomson, J.M., Parker, J., Perou, C.M. & Hammond, S.M. Nat. Methods 1, 47–53 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Exiqon for kindly providing the miRCURY probes. We thank B. Ason, M. Tijsterman and E. Cuppen for reading the manuscript critically. This work was supported by the Council for Earth and Life Sciences of the Netherlands Organization for Scientific Research.

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Correspondence to Ronald H A Plasterk.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Detection of miR-124a, miR-122a and miR-206 with DIG-labeled DNA and LNA probes in 72h zebrafish embryos. (PDF 602 kb)

Supplementary Fig. 2

Determination of the optimal hybridization temperature for in situ detection of miRNAs in the zebrafish embryo. (PDF 3240 kb)

Supplementary Fig. 3

Determination of the optimal hybridization time for in situ detection of miRNAs in the zebrafish embryo. (PDF 1215 kb)

Supplementary Fig. 4

Assessment of the specificity of LNA-modified probes using perfectly matched and mismatched 14-mer and 22-mer LNA-modified probes for miR-124a and miR-206. (PDF 1060 kb)

Supplementary Fig. 5

Detection of miR-183 and miR-217 using LNA-modified probes designed to target the mature, star and loop sequences of the miRNA precursor. (PDF 1303 kb)

Supplementary Fig. 6

In situ hybridizations of miRNAs in Xenopus tropicalis embryos. (PDF 493 kb)

Supplementary Table 1

Short probes, mismatch probes and star and loop probes used in this study. (PDF 79 kb)

Supplementary Table 2

In situ probes and detection of miRNAs in mouse. (PDF 76 kb)

Supplementary Methods (PDF 76 kb)

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Kloosterman, W., Wienholds, E., de Bruijn, E. et al. In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods 3, 27–29 (2006). https://doi.org/10.1038/nmeth843

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  • DOI: https://doi.org/10.1038/nmeth843

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