In situ detection of mature miRNAs in plants using LNA-modified DNA probes

Methods in Molecular Biology

Volumn 883, Issue , 2012, Pages 143-154

  Yao, Xiaozhen ^a   Huang, Hai ^a   Xu, Lin ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

In situ hybridization; LNA modified DNA probe; Plant miRNA

Indexed keywords

LOCKED NUCLEIC ACID; MICRORNA; PLANT RNA; BUFFER; DIGOXIGENIN; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; OLIGONUCLEOTIDE;

ARTICLE; CHEMICAL STRUCTURE; IN SITU HYBRIDIZATION; PRIORITY JOURNAL; RNA ANALYSIS; ARABIDOPSIS; CHEMISTRY; CYTOLOGY; DNA PROBE; GENETICS; HISTOLOGY; METHODOLOGY; MICROTOMY; NUCLEOTIDE SEQUENCE; PLANT LEAF; STAINING;

ARABIDOPSIS; BASE SEQUENCE; BUFFERS; DIGOXIGENIN; DNA PROBES; IN SITU HYBRIDIZATION; INDICATORS AND REAGENTS; MICRORNAS; MICROTOMY; OLIGONUCLEOTIDES; PLANT LEAVES; PLASTIC EMBEDDING; RNA, PLANT; STAINING AND LABELING;

EID: 84865683928     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-839-9_11     Document Type: Article

References (27)

1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
2. Wienholds E, Plasterk RH (2005) MicroRNA function in animal development. FEBS Lett 579:5911-5922
3. Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465-475
4. Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H (2010) siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 38:6883-6894
5. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403:901-906
6. Aukerman MJ, Sakai H (2003) Regulation of fl owering time and fl oral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15:2730-2741
7. Mallory AC, Bartel DP, Bartel B (2005) MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17:1360-1375
8. Yang L, Liu Z, Lu F, Dong A, Huang H (2006) SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J 47:841-850
9. Diederichs S, Haber DA (2007) Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell 131:1097-1108
10. Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O (2004) In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev 18:2237-2242
11. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17:2204-2216
12. Jung JH, Park CM (2007) MIR166/165 genes exhibit dynamic expression patterns in regulating shoot apical meristem and fl oral development in Arabidopsis. Planta 225: 1327-1338
13. Raman S, Greb T, Peaucelle A, Blein T, Laufs P, Theres K (2008) Interplay of miR164, CUPSHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana Plant J 55:65-76
14. Gutierrez L, Bussell JD, Pacurar DI, Schwambach J, Pacurar M, Bellini C (2009) Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Plant Cell 21:3119-3132
15. Yao X, Wang H, Li H, Yuan Z, Li F, Yang L, Huang H (2009) Two types of cis-acting elements control the abaxial epidermis-specifi c transcription of the MIR165a and MIR166a genes. FEBS Lett 583:3711-3717
16. Yoon EK, Yang JH, Lim J, Kim SH, Kim SK, Lee WS (2010) Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res 38:1382-1391
17. Rodriguez JB, Marquez VE, Nicklaus MC, Mitsuya H, Barchi JJ Jr (1994) Conformationally locked nucleoside analogues. Synthesis of dideoxycarbocyclic nucleoside analogues structurally related to neplanocin C. J Med Chem 37:3389-3399
18. Braasch DA, Corey DR (2001) Locked nucleic acid (LNA): fi ne-tuning the recognition of DNA and RNA. Chem Biol 8:1-7
19. Wengel J, Petersen M, Nielsen KE, Jensen GA, Hakansson AE, Kumar R, Sorensen MD, Rajwanshi VK, Bryld T, Jacobsen JP (2001) LNA (locked nucleic acid) and the diastereoisomeric alpha-L-LNA: conformational tuning and high-affi nity recognition of DNA/RNA targets. Nucleosides Nucleotides Nucleic Acids 20:389-396
20. Hakansson AE, Wengel J (2001) The adenine derivative of alpha-L-LNA (alpha-L-ribo confi gured locked nucleic acid): synthesis and high-affi nity hybridization towards DNA, RNA, LNA and alpha-L-LNA complementary sequences. Bioorg Med Chem Lett 11: 935-938
21. Randazzo A, Esposito V, Ohlenschlager O, Ramachandran R, Virgilio A, Mayol L (2005) Structural studies on LNA quadruplexes. Nucleosides Nucleotides Nucleic Acids 24:795-800
22. Valoczi A, Hornyik C, Varga N, Burgyan J, Kauppinen S, Havelda Z (2004) Sensitive and specifi c detection of microRNAs by northern blot analysis using LNA-modifi ed oligonucleotide probes. Nucleic Acids Res 32:e175
23. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH (2005) MicroRNA expression in zebrafi sh embryonic development. Science 309:310-311
24. Kloosterman WP, Wienholds E, de Bruijn E, Kauppinen S, Plasterk RH (2006) In situ detection of miRNAs in animal embryos using LNAmodifi ed oligonucleotide probes. Nat Methods 3:27-29
25. Valoczi A, Varallyay E, Kauppinen S, Burgyan J, Havelda Z (2006) Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. Plant J 47:140-151
26. Long JA, Moan EI, Medford JI, Barton MK (1996) A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis Nature 379:66-69
27. You Y, Moreira BG, Behlke MA, Owczarzy R (2006) Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res 34:e60