Approaches for Studying MicroRNA and Small Interfering RNA Methylation In Vitro and In Vivo

Methods in Enzymology

Volumn 427, Issue , 2007, Pages 139-154

  Yang, Zhiyong ^a   Vilkaitis, Giedrius ^b   Yu, Bin ^a   Klimašauskas, Saulius ^b   Chen, Xuemei ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b VILNIUS UNIVERSITY   (Lithuania)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DICER; GLUTATHIONE TRANSFERASE; MICRORNA; PERIODATE; PLANT EXTRACT; RECOMBINANT HEN1 PROTEIN; RECOMBINANT PROTEIN; RNA METHYLTRANSFERASE; S ADENOSYLMETHIONINE; SMALL INTERFERING RNA; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG; ESCHERICHIA COLI PROTEIN; HEN1 PROTEIN , ESCHERICHIA COLI;

ARABIDOPSIS; BIOGENESIS; ELIMINATION REACTION; EXPRESSION VECTOR; GENE; HEN1 GENE; IMMUNOPRECIPITATION; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; REVIEW; RNA METHYLATION; RNA PROCESSING; ARTICLE; CATALYSIS; GENETICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; METABOLISM; METHYLATION;

ANIMALIA; ARABIDOPSIS;

BLOTTING, NORTHERN; CATALYSIS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; ESCHERICHIA COLI PROTEINS; IMMUNOPRECIPITATION; METHYLATION; MICRORNAS; RECOMBINANT PROTEINS; RNA, SMALL INTERFERING;

EID: 42949086521     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(07)27008-9     Document Type: Review

References (25)

1. Akbergenov R., Si-Ammour A., Blevins T., Amin I., Kutter C., Vanderschuren H., Zhang P., Gruissem W., Meins F., Hohn J.T., and Pooggin M.M. Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res. 34 (2006) 436-444
2. Alefelder S., Patel B.K., and Eckstein F. Incorporation of terminal phosphorothioates into oligonucleotides. Nucleic Acids Res. 26 (1998) 4983-4988
3. Bartel D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
4. Basyuk E., Suavet F., Doglio A., Bordonne R., and Bertrand E. Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res. 31 (2003) 6593-6597
5. Brodersen P., and Voinnet O. The diversity of RNA silencing pathways in plants. Trends Genet. 22 (2006) 268-280
6. Chen X., Liu J., Cheng Y., and Jia D. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129 (2002) 1085-1094
7. Ebhardt H.A., Thi E.P., Wang M.B., and Unrau P.J. Extensive 3′ modification of plant small RNAs is modulated by helper component-proteinase expression. Proc. Natl. Acad. Sci. USA 102 (2005) 13398-13403
8. Grishok A., Pasquinelli A.E., Conte D., Li N., Parrish S., Ha I., Baillie D.L., Fire A., Ruvkun G., and Mello C.C. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106 (2001) 23-34
9. Hutvágner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., and Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293 (2001) 834-838
10. Jacobsen S.E., Running M., and Meyerowitz E.M. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development 126 (1999) 5231-5243
11. Ketting R.F., Fischer S.E., Bernstein E., Sijen T., Hannon G.J., and Plasterk R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15 (2001) 2654-2659
12. Kumar S., Cheng X., Pflugrath J.W., and Roberts R.J. Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex. Biochemistry 31 (1992) 8648-8653
13. Kurihara Y., and Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like1 protein functions. Proc. Natl. Acad. Sci. USA 101 (2004) 12753-12758
14. Lee R.C., Feinbaum R.C., and Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 (1993) 843-854
15. Lee Y., Ahn C., Han J., Choi H., Kim J., Yim J., Lee J., Provost P., Radmark O., Kim S., and Kim V.N. The nuclear RNase III Drosha initiates microRNA processing. Nature 425 (2003) 415-419
16. Lee Y., Jeon K., Lee J.T., Kim S., and Kim V.N. MicroRNA maturation: Stepwise processing and subcellular localization. EMBO J. 21 (2002) 4663-4670
17. Li J., Yang Z., Yu B., Liu J., and Chen X. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol. 15 (2005) 1501-1507
18. Park W., Li J., Song R., Messing J., and Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12 (2002) 1484-1495
19. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., and Bartel D.P. MicroRNAs in plants. Genes Dev. 16 (2002) 1616-1626
20. Vaucheret H. Post-transcriptional small RNA pathways in plants: Mechanisms and regulations. Genes Dev. 20 (2006) 759-771
21. Vilkaitis G., Merkiene E., Serva S., Weinhold E., and Klimasauskas S. The mechanism of DNA cytosine-5 methylation: Kinetic and mutational dissection of HhaI methyltransferase. J. Biol. Chem. 276 (2001) 20924-20934
22. Tkaczuk K.L., Obarska A., and Bujnicki J.M. Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol. Biol. 6 (2006) 6
23. Yang J., Trakselis M.A., Roccasecca R.M., and Benkovic S.J. The application of a minicircle substrate in the study of the coordinated T4 DNA replication. J. Biol. Chem. 278 (2003) 49828-49838
24. Yang Z., Ebright Y.W., Yu B., and Chen X. HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res. 34 (2006) 667-675
25. Yu B., Yang Z., Li J., Minakhina S., Yang M., Padgett R.W., Steward R., and Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science 307 (2005) 932-935