A comprehensive analysis of precursor microRNA cleavage by human Dicer

RNA

Volumn 18, Issue 11, 2012, Pages 2083-2092

  Feng, Yong ^a,b   Zhang, Xiaoxiao ^a   Graves, Paul ^c   Zeng, Yan ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b WUHAN UNIVERSITY   (China)

^c NEW YORK METHODIST HOSPITAL   (United States)

Author keywords

Dicer; pre miRNA; RNA binding; RNA processing; Secondary structure

Indexed keywords

DICER; MICRORNA; NUCLEASE S1; RNA PRECURSOR;

ARTICLE; BINDING ASSAY; ENZYME ACTIVITY; GEL MOBILITY SHIFT ASSAY; GENETIC VARIABILITY; HUMAN; HUMAN CELL; IN VITRO STUDY; PRIORITY JOURNAL; PROTEIN CLEAVAGE; RNA BINDING; RNA CLEAVAGE; RNA STRUCTURE;

BASE SEQUENCE; DEAD-BOX RNA HELICASES; ELECTROPHORETIC MOBILITY SHIFT ASSAY; FUNGAL PROTEINS; HEK293 CELLS; HUMANS; INVERTED REPEAT SEQUENCES; KINETICS; MICRORNAS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; RIBONUCLEASE III; RNA CLEAVAGE; RNA PRECURSORS; SINGLE-STRAND SPECIFIC DNA AND RNA ENDONUCLEASES; SUBSTRATE SPECIFICITY;

EID: 84867681364     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.033688.112     Document Type: Article

References (30)

1. Bartel DP. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
2. Chakravarthy S, Sternberg SH, Kellenberger CA, Doudna JA. 2010. Substrate-specific kinetics of Dicer-catalyzed RNA processing. J Mol Biol 404: 392-402.
3. Du Z, Lee JK, Tjhen R, Stroud RM, James TL. 2008. Structural and biochemical insights into the dicing mechanism of mouse Dicer: A conserved lysine is critical for dsRNA cleavage. Proc Natl Acad Sci 105: 2391-2396. (Pubitemid 351520524)
4. Feng Y, Zhang X, Song Q, Li T, Zeng Y. 2011. Drosha processing controls the specificity and efficiency of global microRNA expression. Biochim Biophys Acta 1809: 700-707.
5. Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X. 2006. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 124: 355-366. (Pubitemid 43121983)
6. Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X. 2008. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol 67: 143-154. (Pubitemid 350231141)
7. Koscianska E, Starega-Roslan J, Krzyzosiak WJ. 2011. The role of Dicer protein partners in the processing of microRNA precursors. PLoS ONE 6: e28548. doi: 10.1371/journal.pone.0028548.
8. Kozomara A, Griffiths-Jones S. 2011. miRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157.
9. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, et al. 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414. (Pubitemid 46970709)
10. Lau PW, Guiley KZ, De N, Potter CS, Carragher B. 2012. The molecular architecture of human Dicer. Nat Struct Mol Biol 19: 436-440.
11. Lavoie M, Abou Elela S. 2008. Yeast ribonuclease III uses a network of multiple hydrogen bonds for RNA binding and cleavage. Biochemistry 47: 8514-8526.
12. Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ, Carthew RW. 2004. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117: 69-81. (Pubitemid 38469899)
13. Ma JB, Ye K, Patel DJ. 2004. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429: 318-322. (Pubitemid 38684819)
14. Ma E, MacRae IJ, Kirsch JF, Doudna JA. 2008. Autoinhibition of human Dicer by its internal helicase domain. J Mol Biol 380: 237-243.
15. MacRae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. 2006. Structural basis for double-stranded RNA processing by Dicer. Science 311: 195-198. (Pubitemid 43108178)
16. MacRae IJ, Zhou K, Doudna JA. 2007. Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol 14: 934-940. (Pubitemid 47525174)
17. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15: 8783-8798.
18. Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN. 2011. Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature 475: 201-205.
19. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B, Radmark O. 2002. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J 21: 5864-5874. (Pubitemid 35315284)
20. Sashital DG, Doudna JA. 2010. Structural insights into RNA interference. Curr Opin Struct Biol 20: 90-97.
21. Starega-Roslan J, Krol J, Koscianska E, Kozlowski P, Szlachcic WJ, Sobczak K, Krzyzosiak WJ. 2011. Structural basis of microRNA length variety. Nucleic Acids Res 39: 257-268.
22. Tsutsumi A, Kawamata T, Izumi N, Seitz H, Tomari Y. 2011. Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat Struct Mol Biol 18: 1153-1158.
23. Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A. 2005. The contributions of dsRNA structure to Dicer specificity and efficiency. RNA 11: 674-682. (Pubitemid 40594334)
24. Wang Z, Hartman E, Roy K, Chanfreau G, Feigon J. 2011. Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs. Structure 19: 999-1010.
25. Welker NC, Maity TS, Ye X, Aruscavage PJ, Krauchuk AA, Liu Q, Bass BL. 2011. Dicer's helicase domain discriminates dsRNA termini to promote an altered reaction mode. Mol Cell 41: 589-599.
26. Zeng Y, Yi R, Cullen BR. 2005. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J 24: 138-148. (Pubitemid 40188471)
27. Zhang X, Zeng Y. 2010. The terminal loop region controls microRNA processing by Drosha and Dicer. Nucleic Acids Res 38: 7689-7697.
28. Zhang H, Kolb FA, Brondani V, Billy E, Filipowicz W. 2002. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J 21: 5875-5885. (Pubitemid 35315285)
29. Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W. 2004. Single processing center models for human Dicer and bacterial RNase III. Cell 118: 57-68. (Pubitemid 38902814)
30. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)