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PMID: 18042455 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2.

Molecular cell ·Vol. 28 ·No. 4 ·2007-11-30 ·Pages 598-613

Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, Sewell AK, Liu X, Yates JR, Han M

Abstract

MicroRNAs (miRNAs) regulate gene expression for diverse functions, but only a limited number of mRNA targets have been experimentally identified. We show that GW182 family proteins AIN-1 and AIN-2 act redundantly to regulate the expression of miRNA targets, but not miRNA biogenesis. Immunoprecipitation (IP) and mass spectrometry indicate that AIN-1 and AIN-2 interact only with miRNA-specific Argonaute proteins ALG-1 and ALG-2 and with components of the core translational initiation complex. Known miRNA targets are enriched in AIN-2 complexes, correlating with the expression of corresponding miRNAs. Combining IP with pyrosequencing and microarray analysis of RNAs associated with AIN-1/AIN-2, we identified 106 previously annotated miRNAs plus nine new candidate miRNAs, but nearly no siRNAs, and more than 3500 potential miRNA targets, including nearly all known ones. Our results demonstrate an effective biochemical approach to systematically identify miRNA targets and provide valuable insights regarding the properties of miRNA effector complexes.

MeSH Terms
3' Untranslated Regions/metabolism Animals Base Sequence Caenorhabditis elegans/cytology,embryology,enzymology,genetics Caenorhabditis elegans Proteins/genetics,metabolism Carrier Proteins/genetics,metabolism Endoribonucleases/metabolism Eukaryotic Initiation Factor-4E/metabolism Gene Expression Regulation, Developmental MicroRNAs/metabolism Molecular Sequence Data Mutation/genetics Protein Binding Protein Biosynthesis RNA Caps/metabolism RNA, Helminth/isolation & purification,metabolism RNA, Messenger/genetics,metabolism RNA, Small Interfering/metabolism RNA-Induced Silencing Complex/metabolism Sequence Analysis, RNA Time Factors
Chemicals
3' Untranslated Regions AIN-1 protein, C elegans AIN-2 protein, C elegans Caenorhabditis elegans Proteins Carrier Proteins Eukaryotic Initiation Factor-4E MicroRNAs RNA Caps RNA, Helminth RNA, Messenger RNA, Small Interfering RNA-Induced Silencing Complex Endoribonucleases
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Zhang Liang
Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO 80309, USA.
Ding Lei
Cheung Tom H
Dong Meng-Qiu
Chen Jun
Sewell Aileen K
Liu Xuedong
Yates John R
Han Min
References (66)
66 references, click to expand
  1. Combinatorial microRNA target predictions.
    Nat Genet. 2005 May;37(5):495-500 PMID: 15806104
  2. Genome sequencing in microfabricated high-density picolitre reactors.
    Nature. 2005 Sep 15;437(7057):376-80 PMID: 16056220
  3. The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans.
    Mol Cell. 2005 Aug 19;19(4):437-47 PMID: 16109369
  4. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.
    Cell. 2005 Jan 14;120(1):15-20 PMID: 15652477
  5. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
    Genes Dev. 2006 Jul 15;20(14):1885-98 PMID: 16815998
  6. Inhibition of translational initiation by Let-7 MicroRNA in human cells.
    Science. 2005 Sep 2;309(5740):1573-6 PMID: 16081698
  7. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation.
    Dev Biol. 2002 Mar 15;243(2):215-25 PMID: 11884032
  8. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans.
    Nature. 2003 Dec 18;426(6968):845-9 PMID: 14685240
  9. The STAR protein, GLD-1, is a translational regulator of sexual identity in Caenorhabditis elegans.
    EMBO J. 1999 Jan 4;18(1):258-69 PMID: 9878068
  10. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs.
    Mol Cell. 2004 Jul 23;15(2):185-97 PMID: 15260970
  11. Ballistic transformation of Caenorhabditis elegans.
    Gene. 1999 Mar 18;229(1-2):31-5 PMID: 10095101
  12. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans.
    Nature. 2000 Feb 24;403(6772):901-6 PMID: 10706289
  13. The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target.
    Dev Cell. 2003 May;4(5):639-50 PMID: 12737800
  14. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6 PMID: 16845052
  15. A micrococcal nuclease homologue in RNAi effector complexes.
    Nature. 2003 Sep 25;425(6956):411-4 PMID: 14508492
  16. MicroRNAs and other tiny endogenous RNAs in C. elegans.
    Curr Biol. 2003 May 13;13(10):807-18 PMID: 12747828
  17. MicroRNA functions in animal development and human disease.
    Development. 2005 Nov;132(21):4653-62 PMID: 16224045
  18. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing.
    RNA. 2005 Nov;11(11):1640-7 PMID: 16177138
  19. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.
    Cell. 2006 Dec 15;127(6):1193-207 PMID: 17174894
  20. A role for the P-body component GW182 in microRNA function.
    Nat Cell Biol. 2005 Dec;7(12):1261-6 PMID: 16284623
  21. Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells.
    Annu Rev Biochem. 1996;65:693-739 PMID: 8811193
  22. microRNA target predictions in animals.
    Nat Genet. 2006 Jun;38 Suppl:S8-13 PMID: 16736023
  23. Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression.
    Genome Biol. 2003;4(7):223 PMID: 12844354
  24. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA.
    Cell. 1997 Mar 7;88(5):637-46 PMID: 9054503
  25. Disruption of GW bodies impairs mammalian RNA interference.
    Nat Cell Biol. 2005 Dec;7(12):1267-74 PMID: 16284622
  26. Identification of novel argonaute-associated proteins.
    Curr Biol. 2005 Dec 6;15(23):2149-55 PMID: 16289642
  27. The diverse functions of microRNAs in animal development and disease.
    Dev Cell. 2006 Oct;11(4):441-50 PMID: 17011485
  28. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.
    Cell. 1993 Dec 3;75(5):843-54 PMID: 8252621
  29. Evidence that microRNAs are associated with translating messenger RNAs in human cells.
    Nat Struct Mol Biol. 2006 Dec;13(12):1102-7 PMID: 17128271
  30. The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans.
    Dev Cell. 2005 Sep;9(3):403-14 PMID: 16139228
  31. The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs.
    Dev Cell. 2003 May;4(5):625-37 PMID: 12737799
  32. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans.
    Cell. 1993 Dec 3;75(5):855-62 PMID: 8252622
  33. Caenorhabditis elegans nucleoporins Nup93 and Nup205 determine the limit of nuclear pore complex size exclusion in vivo.
    Mol Biol Cell. 2003 Dec;14(12):5104-15 PMID: 12937276
  34. Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
    Nat Biotechnol. 2001 Mar;19(3):242-7 PMID: 11231557
  35. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
    J Mol Biol. 1999 May 21;288(5):911-40 PMID: 10329189
  36. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation.
    Dev Biol. 1999 Dec 15;216(2):671-80 PMID: 10642801
  37. Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions.
    Nat Struct Mol Biol. 2006 Sep;13(9):849-51 PMID: 16921378
  38. The mir-84 and let-7 paralogous microRNA genes of Caenorhabditis elegans direct the cessation of molting via the conserved nuclear hormone receptors NHR-23 and NHR-25.
    Development. 2006 Dec;133(23):4631-41 PMID: 17065234
  39. Mfold web server for nucleic acid folding and hybridization prediction.
    Nucleic Acids Res. 2003 Jul 1;31(13):3406-15 PMID: 12824337
  40. Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. elegans germ cell development.
    Genes Dev. 2001 Sep 15;15(18):2408-20 PMID: 11562350
  41. Micro RNAs in animal development.
    Cell. 2006 Mar 10;124(5):877-81 PMID: 16530032
  42. An mRNA m7G cap binding-like motif within human Ago2 represses translation.
    Cell. 2007 Jun 15;129(6):1141-51 PMID: 17524464
  43. Short RNAs repress translation after initiation in mammalian cells.
    Mol Cell. 2006 Feb 17;21(4):533-42 PMID: 16483934
  44. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing.
    Cell. 2001 Jul 13;106(1):23-34 PMID: 11461699
  45. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans.
    Cell. 2002 Jun 28;109(7):861-71 PMID: 12110183
  46. Isolation of microRNA targets by miRNP immunopurification.
    RNA. 2007 Aug;13(8):1198-204 PMID: 17592038
  47. Translational control of maternal RNAs.
    WormBook. 2005 Nov 10;:1-11 PMID: 18050410
  48. Human let-7a miRNA blocks protein production on actively translating polyribosomes.
    Nat Struct Mol Biol. 2006 Dec;13(12):1108-14 PMID: 17128272
  49. Yeast proteins related to the p40/laminin receptor precursor are required for 20S ribosomal RNA processing and the maturation of 40S ribosomal subunits.
    Cancer Res. 1999 Feb 1;59(3):704-10 PMID: 9973221
  50. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi.
    Cell. 2006 Nov 17;127(4):747-57 PMID: 17110334
  51. Cell fates and fusion in the C. elegans vulval primordium are regulated by the EGL-18 and ELT-6 GATA factors -- apparent direct targets of the LIN-39 Hox protein.
    Development. 2002 Nov;129(22):5171-80 PMID: 12399309
  52. Identification of human microRNA targets from isolated argonaute protein complexes.
    RNA Biol. 2007 Jun;4(2):76-84 PMID: 17637574
  53. Argonaute2 is the catalytic engine of mammalian RNAi.
    Science. 2004 Sep 3;305(5689):1437-41 PMID: 15284456
  54. Cytosolic aconitase and ferritin are regulated by iron in Caenorhabditis elegans.
    J Biol Chem. 2003 Jan 31;278(5):3227-34 PMID: 12438312
  55. A genome-wide map of conserved microRNA targets in C. elegans.
    Curr Biol. 2006 Mar 7;16(5):460-71 PMID: 16458514
  56. A Caenorhabditis elegans homologue of hunchback is required for late stages of development but not early embryonic patterning.
    Dev Biol. 1999 Jan 15;205(2):240-53 PMID: 9917360
  57. Multiple mechanisms are involved in regulating the expression of the developmental timing regulator lin-28 in Caenorhabditis elegans.
    EMBO J. 2006 Dec 13;25(24):5794-804 PMID: 17139256
  58. MicroRNA silencing through RISC recruitment of eIF6.
    Nature. 2007 Jun 14;447(7146):823-8 PMID: 17507929
  59. MicroRNAs: genomics, biogenesis, mechanism, and function.
    Cell. 2004 Jan 23;116(2):281-97 PMID: 14744438
  60. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation.
    Cell. 2005 Aug 26;122(4):553-63 PMID: 16122423
  61. Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning.
    Methods Mol Biol. 2004;265:131-58 PMID: 15103073
  62. Translation of a small subset of Caenorhabditis elegans mRNAs is dependent on a specific eukaryotic translation initiation factor 4E isoform.
    Mol Cell Biol. 2005 Jan;25(1):100-13 PMID: 15601834
  63. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor.
    Mol Cell. 2000 Apr;5(4):659-69 PMID: 10882102
  64. The timing of lin-4 RNA accumulation controls the timing of postembryonic developmental events in Caenorhabditis elegans.
    Dev Biol. 1999 Jun 1;210(1):87-95 PMID: 10364429
  65. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.
    Cell. 2006 Sep 22;126(6):1203-17 PMID: 16990141
  66. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans.
    Nature. 2002 Aug 29;418(6901):975-9 PMID: 12214599
Article Info
Journal
Molecular cell
Abbr.
Mol Cell
ISSN
1097-2765
DOI
10.1016/j.molcel.2007.09.014
Published
2007-11-30
Pages
598-613
Language
English
Region
United States
NLM ID
9802571
PMCID
PMC2186060
Subset
IM
Grants
NIGMS NIH HHS · R01 GM047869 · United States
NIGMS NIH HHS · R01 GM047869-15 · United States
NCRR NIH HHS · P41 RR011823 · United States
NCRR NIH HHS · P41 RR11823 · United States
NIGMS NIH HHS · GM47869 · United States
Databases
GENBANK
AAC24251
GEO
GSE9073
External Links
PubMed source DOI: 10.1016/j.molcel.2007.09.014 PMC Full Text View journal details
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