MicroRNA–Directed siRNA Biogenesis in

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RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi–related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.

Vyšlo v časopise: MicroRNA–Directed siRNA Biogenesis in. PLoS Genet 6(4): e32767. doi:10.1371/journal.pgen.1000903
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1000903

Souhrn

Zdroje

1. KimVN

HanJ

SiomiMC

2009 Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10 126 139

2. HutvagnerG

SimardMJ

2008 Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9 22 32

3. JinekM

DoudnaJA

2009 A three-dimensional view of the molecular machinery of RNA interference. Nature 457 405 412

4. MatrangaC

TomariY

ShinC

BartelDP

ZamorePD

2005 Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123 607 620

5. ChapmanEJ

CarringtonJC

2007 Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8 884 896

6. GrishokA

PasquinelliAE

ConteD

LiN

ParrishS

2001 Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106 23 34

7. SteinerFA

OkiharaKL

HoogstrateSW

SijenT

KettingRF

2009 RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans. Nat Struct Mol Biol 16 207 211

8. HanT

ManoharanAP

HarkinsTT

BouffardP

FitzpatrickC

2009 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans. Proc Natl Acad Sci U S A 106 18674 18679

9. SijenT

FleenorJ

SimmerF

ThijssenKL

ParrishS

2001 On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107 465 476

10. AokiK

MoriguchiH

YoshiokaT

OkawaK

TabaraH

2007 In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J 26 5007 5019

11. PakJ

FireA

2007 Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315 241 244

12. SijenT

SteinerFA

ThijssenKL

PlasterkRH

2007 Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315 244 247

13. VoinnetO

2008 Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci 13 317 328

14. YigitE

BatistaPJ

BeiY

PangKM

ChenCC

2006 Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 127 747 757

15. SteinerFA

HoogstrateSW

OkiharaKL

ThijssenKL

KettingRF

2007 Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nat Struct Mol Biol 14 927 933

16. TabaraH

YigitE

SiomiH

MelloCC

2002 The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell 109 861 871

17. TopsBB

PlasterkRH

KettingRF

2006 The Caenorhabditis elegans Argonautes ALG-1 and ALG-2: almost identical yet different. Cold Spring Harb Symp Quant Biol 71 189 194

18. RubyJG

JanC

PlayerC

AxtellMJ

LeeW

2006 Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127 1193 1207

19. LabeitS

KolmererB

1995 Titins: giant proteins in charge of muscle ultrastructure and elasticity. Science 270 293 296

20. FraserAG

KamathRS

ZipperlenP

Martinez-CamposM

SohrmannM

2000 Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408 325 330

21. RualJF

CeronJ

KorethJ

HaoT

NicotAS

2004 Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 14 2162 2168

22. SonnichsenB

KoskiLB

WalshA

MarschallP

NeumannB

2005 Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434 462 469

23. LimLP

LauNC

WeinsteinEG

AbdelhakimA

YektaS

2003 The microRNAs of Caenorhabditis elegans. Genes Dev 17 991 1008

24. MartinezNJ

OwMC

Reece-HoyesJS

BarrasaMI

AmbrosVR

2008 Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 18 2005 2015

25. GuW

ShirayamaM

ConteDJr

VasaleJ

BatistaPJ

2009 Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell 36 231 244

26. WelkerNC

HabigJW

BassBL

2007 Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes. RNA 13 1090 1102

27. BaileyTL

ElkanC

1994 Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2 28 36

28. DuchaineTF

WohlschlegelJA

KennedyS

BeiY

ConteDJr

2006 Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 124 343 354

29. MlotshwaS

PrussGJ

VanceV

2008 Small RNAs in viral infection and host defense. Trends Plant Sci 13 375 382

30. AllenE

XieZ

GustafsonAM

CarringtonJC

2005 microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121 207 221

31. YoshikawaM

PeragineA

ParkMY

PoethigRS

2005 A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19 2164 2175

32. AllenE

XieZ

GustafsonAM

SungGH

SpataforaJW

2004 Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36 1282 1290

33. RajagopalanR

VaucheretH

TrejoJ

BartelDP

2006 A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20 3407 3425

34. FahlgrenN

HowellMD

KasschauKD

ChapmanEJ

SullivanCM

2007 High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2 e219 doi:10.1371/journal.pone.0000219

35. SvobodaP

Di CaraA

2006 Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci 63 901 908

36. FelippesFF

SchneebergerK

DezulianT

HusonDH

WeigelD

2008 Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14 2455 2459

37. LimLP

LauNC

Garrett-EngeleP