Structure of precursor microRNA’s terminal loop regulates human Dicer’s dicing activity by switching DExH/D domain

Protein and Cell

Volumn 6, Issue 3, 2015, Pages 185-193

  Liu, Zhongmin ^a,b   Wang, Jia ^b   Li, Gang ^a   Wang, Hong Wei ^b  

^a PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

^b TSINGHUA UNIVERSITY   (China)

Author keywords

A to I editing; DExH D (ATPase helicase) domain; human Dicer; pre miRNA 151; single particle electron microscopy

Indexed keywords

ADAR1P110 PROTEIN; ADENOSINE TRIPHOSPHATASE; DICER; HELICASE; MICRORNA; MICRORNA 151; NUCLEIC ACID BINDING PROTEIN; UNCLASSIFIED DRUG; DEAD BOX PROTEIN; RIBONUCLEASE III;

ARTICLE; BACULOVIRUS EXPRESSION SYSTEM; CONFORMATION; CONTROLLED STUDY; ELECTRON MICROSCOPY; ENZYME ACTIVITY; GEL FILTRATION; GEL MOBILITY SHIFT ASSAY; GENE SILENCING; HUMAN; IMAGE PROCESSING; NATIVE POLYACRYLAMIDE GEL ELECTROPHORESIS; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; RNA EDITING; RNA SEQUENCE; RNA STRUCTURE; BASE PAIRING; CHEMISTRY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE;

EUKARYOTA;

BASE PAIRING; BASE SEQUENCE; DEAD-BOX RNA HELICASES; HUMANS; MICRORNAS; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASE III; RNA EDITING;

EID: 84924122348     PISSN: 1674800X     EISSN: 16748018     Source Type: Journal    
DOI: 10.1007/s13238-014-0124-2     Document Type: Article

References (36)

1. Ando Y, Maida Y, Morinaga A, Burroughs AM, Kimura R, Chiba J, Suzuki H, Masutomi K, Hayashizaki Y (2011) Two-step cleavage of hairpin RNA with 5’ overhangs by human DICER. BMC Mol Biol 12:6
2. Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR (2006) RNA editing of human microRNAs. Genome Biol 7:R27
3. Brennicke A, Marchfelder A, Binder S (1999) RNA editing. FEMS Microbiol Rev 23:297–316
4. Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655
5. Castilla-Llorente V, Nicastro G, Ramos A (2013) Terminal loop-mediated regulation of miRNA biogenesis: selectivity and mechanisms. Biochem Soc Trans 41:861–865
6. Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436:740–744
7. Das AK, Carmichael GG (2007) ADAR editing wobbles the microRNA world. ACS Chem Biol 2:217–220
8. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158
9. Gu S, Jin L, Zhang Y, Huang Y, Zhang F, Valdmanis PN, Kay MA (2012) The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo. Cell 151:900–911
10. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5:522–531
11. Heo I, Joo C, Cho J, Ha M, Han J, Kim VN (2008) Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell 32:276–284
12. Heo I, Ha M, Lim J, Yoon MJ, Park JE, Kwon SC, Chang H, Kim VN (2012) Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell 151:521–532
13. Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R, Nishikura K (2007a) RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer–TRBP complex. EMBO Rep 8:763–769
14. Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K (2007b) Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315:1137–1140
15. Lau P-W, Guiley KZ, De N, Potter CS, Carragher B, MacRae IJ (2012) The molecular architecture of human Dicer. Nat Struct Mol Biol 19:436–440
16. Lee Y, Hur I, Park S-Y, Kim Y-K, Suh MR, Kim AVN (2006) The role of PACT in the RNA silencing pathway. EMBO J 25:522–532
17. Ma E, MacRae IJ, Kirsch JF, Doudna JA (2008) Autoinhibition of human dicer by its internal helicase domain. J Mol Biol 380:237–243
18. MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA (2008) In vitro reconstitution of the human RISC-loading complex. Proc Natl Acad Sci USA 105(2):512–517
19. Nishikura K (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321–349
20. Ota H, Sakurai M, Gupta R, Valente L, Wulff BE, Ariyoshi K, Iizasa H, Davuluri RV, Nishikura K (2013) ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing. Cell 153:575–589
21. 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
22. Scheres SHW (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530
23. Schraml E, Grillari J (2012) From cellular senescence to age associated diseases: the miRNA connection. Longev Heal 1:1–15
24. Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc 3:1941–1974
25. Su AAH, Randau L (2011) A-to-I and C-to-U editing within transfer RNAs. Biochemistry 76:932–937
26. Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol 157:38–46
27. Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA, Wang H-W (2013) Substrate-specific structural rearrangements of human Dicer. Nat Struct Mol Biol 20:662–670
28. 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
29. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the IMAGIC image processing system. J Struct Biol 116:17–24
30. Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma E, Felderer K, Doudna JA, Nogales E (2009) Structural insights into RNA processing by the human RISC-loading complex. Nat Struct Mol Biol 16:1148–1153
31. Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, Sestan N, Steitz JA (2013) Mammalian 5′-capped microRNA precursors that generate a single microRNA. Cell 155:1568–1580
32. Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R, Nishikura K (2006) Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 13:13–21
33. Zhang X, Zeng Y (2010) The terminal loop region controls microRNA processing by Drosha and Dicer. Nucleic Acids Res 38:7689–7697
34. Zhang H, Kolb FA, Vincent Brondani EBA, Filipowicz W (2002) Human Dicer preferentially cleaves dsRNAs at their termini without ATP. EMBO J 21:5875–5885
35. 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
36. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415