Whole mount in situ hybridization detection of mRNAs using short LNA containing DNA oligonucleotide probes

RNA

Volumn 16, Issue 3, 2010, Pages 632-637

  Darnell, Diana K ^a   Stanislaw, Stacey ^a   Kaur, Simran ^a   Antin, Parker B ^a,b  

^a UNIVERSITY OF ARIZONA   (United States)

^b University of Arizona   (United States)

Author keywords

Chicken embryo; In situ hybridization; Locked nucleic acids, LNA; mRNA detection

Indexed keywords

COMPLEMENTARY DNA; COMPLEMENTARY RNA; DNA; LOCKED NUCLEIC ACID; MESSENGER RNA; OLIGONUCLEOTIDE;

ALTERNATIVE RNA SPLICING; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CHICK EMBRYO; COMPUTER MODEL; CONTROLLED STUDY; DNA PROBE; DNA TEMPLATE; EMBRYO; EMBRYONAL TISSUE; EXON; FEMALE; FLUORESCENCE; IN SITU HYBRIDIZATION; NONHUMAN; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; RNA PROBE; SYNTHESIS; TRANSCRIPTION REGULATION;

ALTERNATIVE SPLICING; ANIMALS; CHICK EMBRYO; GENETIC TECHNIQUES; IN SITU HYBRIDIZATION; MUSCLE PROTEINS; OLIGONUCLEOTIDES; RNA, MESSENGER;

EID: 77149131534     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1775610     Document Type: Article

References (30)

1. Alsan BH, Schultheiss TM. 2002. Regulation of avian cardiogenesis by Fgf8 signaling. Development 129: 1935-1943.
2. Antin PB, Zhang W, Bales MA, Garriock R, Yatskievych TA. 2002. Precocious expression of cardiac troponin T during early avian embryogenesis. Dev Dyn 225: 135-141.
3. Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, Wittbrodt J, Antin PB, Plasterk RH. 2006. Differences in vertebrate microRNA expression. Proc Natl Acad Sci 103: 14385-14389.
4. Cooper TA, Ordahl CP. 1984. A single troponin T gene regulated by different programs in cardiac and skeletal muscle development. Science 226: 979-982.
5. Darnell DK, Kaur S, Stanislaw S, Konieczka JK, Yatskievych TA, Antin PB. 2006. MicroRNA expression during chick embryo development. Dev Dyn 236: 3156-3165.
6. Dorkin TJ, Robinson MC, Marsh C, Bjartell A, Neal DE, Leung HY. 1999. FGF8 over-expression in prostate cancer is associated with decreased patient survival and persists in androgen independent disease. Oncogene 18: 2755-2761.
7. Gimeno L, Martinez S. 2007. Expression of chick Fgf19 and mouse Fgf15 orthologs is regulated in the developing brain by Fgf8 and Shh. Dev Dyn 236: 2285-2297.
8. Jacobsen N, Bentzen J, Meldgaard M, Jakobsen MH, Fenger M, Kauppinen S, Skouv J. 2002. LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E. Nucleic Acids Res 30: e100.
9. Johnson MP, Haupt LM, Griffiths LR. 2004. Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res 32: e55.
10. Johnson CD, Esquela-Kerscher A, Stefani G, Byrom M, Kelnar K, Ovcharenko D, Wilson M, Wang X, Shelton J, Shingara J, et al. 2007. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res 67: 7713-7722.
11. Karabagli H, Karabagli P, Ladher R, Schoenwolf G. 2002a. Comparison of the expression patterns of several fibroblast growth factors during chick gastrulation and neurulation. Anat Embryol (Berl) 205: 365-370.
12. Karabagli H, Karabagli P, Ladher RK, Schoenwolf GC. 2002b. Survey of fibroblast growth factor expression during chick organogenesis. Anat Rec 268: 1-6.
13. Kloosterman W, Wienholds E, De Bruijn E, Kauppinen S, Plasterk R. 2006. In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods 3: 27-29.
14. Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE, Wengel J. 1998. LNA (locked nucleic acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine, and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54: 3607-3630.
15. Ladher RK, Church VL, Allen S, Robson L, Abdelfattah A, Brown NA, Hattersley G, Rosen V, Luyten FP, Dale L, et al. 2000. Cloning and expression of the Wnt antagonists Sfrp-2 and Frzb during chick development. Dev Biol 218: 183-198.
16. Latorra D, Campbell K, Wolter A, Hurley JM. 2003. Enhanced allelespecific PCR discrimination in SNP genotyping using 39 locked nucleic acid (LNA) primers. Hum Mutat 22: 79-85.
17. Marin F, Nieto MA. 2004. Expression of chicken slug and snail in mesenchymal components of the developing central nervous system. Dev Dyn 230: 144-148.
18. Mctigue PM, Peterson RJ, Kahn JD. 2004. Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA) - DNA duplex formation. Biochemistry 43: 5388-5405.
19. Nelson PT, Baldwin DA, Kloosterman WP, Kauppinen S, Plasterk RH, Mourelatos Z. 2006. RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 12: 187-191.
20. Nieto M. 2002. The snail superfamily of zinc-finger transcription factors. Nat Rev Mol Cell Biol 3: 155-166.
21. Nieto MA, Patel K, Wilkinson DG. 1996. In situ hybridization analysis of chick embryos in whole mount and tissue sections. In Methods in cell biology, Vol 51. Academic Press, New York.
22. Nuovo GJ. 2008. In situ detection of precursor and mature micro-RNAs in paraffin embedded, formalin fixed tissues and cell preparations. Methods 44: 39-46.
23. Obernosterer G, Martinez J, Alenius M. 2007. Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat Protoc 2: 1508-1514.
24. Pena JT, Sohn-Lee C, Rouhanifard SH, Ludwig J, Hafner M, Mihailovic A, Lim C, Holoch D, Berninger P, Zavolan M, et al. 2009. miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods 6: 139-141.
25. Silahtaroglu AN, Nolting D, Dyrskjot L, Berezikov E, Moller M, Tommerup N, Kauppinen S. 2007. Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification. Nat Protoc 2: 2520-2528.
26. Thomsen R. 2005. Dramatically improved RNA in situ hybridization signals using LNA-modified probes. RNA 11: 1745-1748.
27. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-W74.
28. Valoczi A. 2004. Sensitive and specific detection of microRNAs by Northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 32: e175. doi: doi:10.1093/nar/gnh171.
29. Weinholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RHA. 2005. MicroRNA expression in zebrafish embryonic development. Science 309: 310-311.
30. Wengel J, Petersen M, Frieden M, Troels K. 2003. Chemistry of locked nucleic acids (LNA): Design, synthesis, and bio-physical properties. Lett Pept Sci 10: 237-253.