Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

Nature Structural and Molecular Biology

Volumn 20, Issue 9, 2013, Pages 1106-1115

  Zhu, Hongliang ^a,b   Zhou, Yuyi ^a,b   Castillo González, Claudia ^a   Lu, Amber ^a   Ge, Chunxiao ^a   Zhao, Ying Tao ^c   Duan, Liusheng ^b   Li, Zhaohu ^b   Axtell, Michael J ^d,e   Wang, Xiu Jie ^c   Zhang, Xiuren ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b CHINA AGRICULTURAL UNIVERSITY   (China)

^c INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DICER; DICER LIKE 1; MICRORNA; PRI MIRNA; RNA HELICASE; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ARABIDOPSIS THALIANA; ARTICLE; BIOGENESIS; CONTROLLED STUDY; GENE EXPRESSION; GENE FUNCTION; GENE REPRESSION; GENE STRUCTURE; NONHUMAN; PLANT GENE; PRI MIR 166 GENE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; RNA PROCESSING; RNA TRANSCRIPTION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; BINDING SITES; CELL CYCLE PROTEINS; MICRORNAS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NUCLEIC ACID CONFORMATION; PLANTS, GENETICALLY MODIFIED; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASE III; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA STABILITY; RNA, PLANT;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 84883739493     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2646     Document Type: Article

References (44)

1. Kim, V.N., Han, J. & Siomi, M.C. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10, 126-139 (2009).
2. Han, J. et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125, 887-901 (2006). (Pubitemid 43810154)
3. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
4. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437-1441 (2004). (Pubitemid 39167657)
5. Voinnet, O. Origin, biogenesis and activity of plant microRNAs. Cell 136, 669-687 (2009).
6. Guo, H., Ingolia, N.T., Weissman, J.S. & Bartel, D.P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835-840 (2010).
7. Czech, B. & Hannon, G.J. Small RNA sorting: matchmaking for Argonautes. Nat. Rev. Genet. 12, 19-31 (2011).
8. Bazzini, A.A., Lee, M. & Giraldez, A. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336, 233-237 (2012).
9. Djuranovic, S., Nahvi, A. & Green, R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237-240 (2012).
10. Li, S. et al. MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153, 562-574 (2013).
11. Chen, X. Plant microRNAs at a glance. Semin. Cell Dev. Biol. 21, 781 (2010).
12. Ren, G. et al. Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc. Natl. Acad. Sci. USA 109, 12817-12821 (2012).
13. Machida, S., Chen, H. & Yuan, A. Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE. Nucleic Acids Res. 39, 7828-7836 (2011).
14. Yang, S.W. et al. Structure of Arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing. Structure 18, 594-605 (2010).
15. Dong, Z., Han, M. & Fedoroff, N. The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc. Natl. Acad. Sci. USA 105, 9970-9975 (2008).
16. Grigg, S.P., Canales, C., Hay, A. & Tsiantis, M. SERRATE coordinates shoot meristem function and leaf axial patterning in Arabidopsis. Nature 437, 1022-1026 (2005). (Pubitemid 41486983)
17. Han, M.H., Goud, S., Song, L. & Fedoroff, N. The Arabidopsis double-stranded RNA binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. USA 101, 1093-1098 (2004). (Pubitemid 38160589)
18. Kurihara, Y., Takashi, Y. & Watanabe, Y. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12, 206-212 (2006). (Pubitemid 43121925)
19. Lobbes, D., Rallapalli, G., Schmidt, D., Martin, C. & Clarke, J. SERRATE: a new player on the plant microRNA scene. EMBO Rep. 7, 1052-1058 (2006). (Pubitemid 44480523)
20. Vazquez, F., Gasciolli, V., Crete, P. & Vaucheret, H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 14, 346-351 (2004). (Pubitemid 38300215)
21. Hirsch, J. et al. Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol. 140, 1192-1204 (2006). (Pubitemid 43956207)
22. Xie, Z. et al. Expression of Arabidopsis MIRNA genes. Plant Physiol. 138, 2145-2154 (2005). (Pubitemid 43733557)
23. Cuperus, J.T. et al. Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc. Natl. Acad. Sci. USA 107, 466-471 (2010).
24. Mateos, J.L., Bologna, N.G., Chorostecki, U. & Palatnik, J.F. Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor. Curr. Biol. 20, 49-54 (2010).
25. Song, L., Axtell, M. & Fedoroff, N. RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Curr. Biol. 20, 37-41 (2010).
26. Werner, S., Wollmann, H., Schneeberger, K. & Weigel, D. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr. Biol. 20, 42-48 (2010).
27. Addo-Quaye, C. et al. Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA 15, 2112-2121 (2009).
28. Bologna, N.G., Mateos, J.L., Bresso, E.G. & Palatnik, J.F. A loop to base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. EMBO J. 28, 3646-3656 (2009).
29. Zhu, H. et al. Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 145, 242-256 (2011).
30. Zhang, Z. & Zhang, X. Argonautes compete for miR165/166 to regulate shoot apical meristem development. Curr. Opin. Plant Biol. 15, 652-658 (2012).
31. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003). (Pubitemid 37442169)
32. Liu, C., Axtell, M.J. & Fedoroff, N.V. The helicase and RNase IIIa domains of Arabidopsis Dicer-like 1 modulate catalytic parameters during microRNA biogenesis. Plant Physiol. 159, 748-758 (2012).
33. Manavella, P.A. et al. Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151, 859-870 (2012).
34. Weinberg, D.E., Kotaro, N.K., Dinshaw J. Patel, D. & Bartel, D. The inside-out mechanism of Dicers from budding yeasts. Cell 146, 262-276 (2011).
35. Gu, S. et al. The loop position of shRNAs and pre-miRNAs is critical for the accuracy of Dicer processing in vivo. Cell 151, 900-911 (2012).
36. Tsutsumi, A., Kawamata, T., Izumi, N., Seitz, H. & Tomari, Y. Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat. Struct. Mol. Biol. 18, 1153-1158 (2011).
37. Addo-Quaye, C., Eshoo, T.W., Bartel, D.P. & Axtell, M.J. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol. 18, 758-762 (2008).
38. German, M.A. et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol. 26, 941-946 (2008).
39. Gregory, B.D. et al. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev. Cell 14, 854-866 (2008).
40. Ma, Z., Coruh, C. & Axtell, M.J. Arabidopsis lyrata small RNAs: transient miRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 22, 1090-1103 (2010).
41. Barrett, T. et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 41, D991-D995 (2013).
42. Zhang, X., Henriques, R., Lin, S.S., Niu, Q. & Chua, N.H. Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral-dip method. Nat. Protoc. 1, 641-646 (2006).
43. Zhang, X. et al. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 20, 3255-3268 (2006). (Pubitemid 44904848)
44. Zhang, X., Garreton, V. & Chua, N.H. The AIP2 E3 ligase acts as a novel negative regulator of ABA signaling by promoting ABI3 degradation. Genes Dev. 19, 1532-1543 (2005). (Pubitemid 41002997)