RNA interference (RNAi)–related pathways affect gene activity by sequence-specific recruitment of Ago proteins to mRNA target molecules. The sequence specificity of this process stems from small RNA (sRNA) co-factors bound by the Ago protein. Stability of sRNA molecules in some pathways is in part regulated by Hen1-mediated methylation of their 3′ ends. Here we describe the effects of the Caenorhabditis elegans HEN1 RNA–methyl-transferase homolog, HENN-1, on the different RNAi pathways in this nematode. We reveal differential effects of HENN-1 on the two pathways that are known to employ methylated sRNA molecules: the 26G and 21U pathways. Surprisingly, in the germline, stability of 21U RNAs, the C. elegans piRNAs, is only mildly affected by loss of methylation; and introduction of artificial 21U target RNA does not further destabilize non-methylated 21U RNAs. In contrast, most 26G RNAs display reduced stability and respond to loss of HENN-1 by displaying increased 3′-uridylation frequencies. Within the 26G RNA class, we find that specifically ERGO-1–bound 26G RNAs are modified by HENN-1, while ALG-3/ALG-4–bound 26G RNAs are not. Global gene expression analysis of henn-1 mutants reveals mild effects, including down-regulation of many germline-expressed genes. Our data suggest that, apart from direct effects of reduced 26G RNA levels of henn-1 on gene expression, most effects on global gene expression are indirect. These studies further refine our understanding of endogenous RNAi in C. elegans and the roles for Hen1 like enzymes in these pathways.
Vyšlo v časopise: Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of. PLoS Genet 8(7): e32767. doi:10.1371/journal.pgen.1002702 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002702
1. MaloneCDHannonGJ 2009 Small RNAs as guardians of the genome. Cell 136 656 668
2. GhildiyalMZamorePD 2009 Small silencing RNAs: an expanding universe. Nat Rev Genet 10 94 108
3. SaitoKSiomiMC 2010 Small RNA-mediated quiescence of transposable elements in animals. Dev Cell 19 687 697
4. BartelDP 2009 MicroRNAs: target recognition and regulatory functions. Cell 136 215 233
5. KettingRF 2011 The many faces of RNAi. Developmental cell 20 148 161
6. HutvagnerGSimardMJ 2008 Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9 22 32
7. EnderCMeisterG 2010 Argonaute proteins at a glance. J Cell Sci 123 1819 1823
8. MiyoshiKMiyoshiTSiomiH 2010 Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production. Molecular genetics and genomics : MGG 284 95 103
9. PakJFireA 2007 Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315 241 244
10. SijenTSteinerFAThijssenKLPlasterkRH 2007 Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315 244 247
11. AokiKMoriguchiHYoshiokaTOkawaKTabaraH 2007 In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J 26 5007 5019
12. YuBYangZLiJMinakhinaSYangM 2005 Methylation as a crucial step in plant microRNA biogenesis. Science 307 932 935
13. HorwichMDLiCMatrangaCVaginVFarleyG 2007 The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr Biol 17 1265 1272
14. SaitoKSakaguchiYSuzukiTSiomiHSiomiMC 2007 Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi - interacting RNAs at their 3′ ends. Genes Dev 21 1603 1608
15. KirinoYMourelatosZ 2007 The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. RNA 13 1397 1401
16. KurthHMMochizukiK 2009 2′-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena. RNA 15 675 685
17. KammingaLMLuteijnMJden BroederMJRedlSKaaijLJ 2010 Hen1 is required for oocyte development and piRNA stability in zebrafish. The EMBO journal 29 3688 3700
18. KawaokaSIzumiNKatsumaSTomariY 2011 3′ End Formation of PIWI-Interacting RNAs In Vitro. Molecular cell 43 1015 1022
19. AmeresSLHorwichMDHungJHXuJGhildiyalM 2010 Target RNA-directed trimming and tailing of small silencing RNAs. Science 328 1534 1539
20. TianYSimanshuDKMaJBPatelDJ 2011 Structural basis for piRNA 2′-O-methylated 3′-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains. Proceedings of the National Academy of Sciences of the United States of America 108 903 910
21. LiJYangZYuBLiuJChenX 2005 Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 15 1501 1507
22. van WolfswinkelJCClaycombJMBatistaPJMelloCCBerezikovE 2009 CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. Cell 139 135 148
23. VasaleJJGuWThiviergeCBatistaPJClaycombJM 2010 Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway. Proc Natl Acad Sci U S A 107 3582 3587
24. HanTManoharanAPHarkinsTTBouffardPFitzpatrickC 2009 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans. Proc Natl Acad Sci U S A 106 18674 18679
25. ConineCCBatistaPJGuWClaycombJMChavesDA 2010 Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans. Proc Natl Acad Sci U S A 107 3588 3593
26. GentJISchvarzsteinMVilleneuveAMGuSGJantschV 2009 A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. Genetics 183 1297 1314
27. PavelecDMLachowiecJDuchaineTFSmithHEKennedyS 2009 Requirement for the ERI/DICER complex in endogenous RNA interference and sperm development in Caenorhabditis elegans. Genetics 183 1283 1295
28. RubyJGJanCPlayerCAxtellMJLeeW 2006 Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127 1193 1207
29. BatistaPJRubyJGClaycombJMChiangRFahlgrenN 2008 PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell 31 67 78
30. DasPPBagijnMPGoldsteinLDWoolfordJRLehrbachNJ 2008 Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell 31 79 90
31. WangGReinkeV 2008 A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr Biol 18 861 867
32. BagijnMPGoldsteinLDSapetschnigAWeickEMBouaskerS 2012 Function, targets and evolution of Caenorhabditis elegans piRNAs. Science: In press
33. GentJILammATPavelecDMManiarJMParameswaranP 2010 Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Mol Cell 37 679 689
34. YigitEBatistaPJBeiYPangKMChenCC 2006 Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 127 747 757
35. GuangSBochnerAFPavelecDMBurkhartKBHardingS 2008 An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321 537 541
36. ClaycombJMBatistaPJPangKMGuWVasaleJJ 2009 The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139 123 134
37. TabaraHSarkissianMKellyWGFleenorJGrishokA 1999 The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99 123 132
38. TkaczukKLObarskaABujnickiJM 2006 Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol 6 6
39. CuppenEGortEHazendonkEMuddeJvan de BeltJ 2007 Efficient target-selected mutagenesis in Caenorhabditis elegans: toward a knockout for every gene. Genome research 17 649 658
40. HuangYJiLHuangQVassylyevDGChenX 2009 Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461 823 827
41. VaginVVSigovaALiCSeitzHGvozdevV 2006 A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313 320 324
42. DuchaineTFWohlschlegelJAKennedySBeiYConteDJr 2006 Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 124 343 354
43. SimmerFTijstermanMParrishSKoushikaSPNonetML 2002 Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Current biology : CB 12 1317 1319
44. LeeRCHammellCMAmbrosV 2006 Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. RNA 12 589 597
45. KennedySWangDRuvkunG 2004 A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427 645 649
46. UpdikeDStromeS 2010 P granule assembly and function in Caenorhabditis elegans germ cells. J Androl 31 53 60
47. KimSKLundJKiralyMDukeKJiangM 2001 A gene expression map for Caenorhabditis elegans. Science 293 2087 2092
48. VastenhouwNLFischerSERobertVJThijssenKLFraserAG 2003 A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Current biology : CB 13 1311 1316
49. KettingRFHaverkampTHvan LuenenHGPlasterkRH 1999 Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99 133 141
50. AmeresSLHungJHXuJWengZZamorePD 2011 Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA 17 54 63
51. BilliACAlessiAFKhivansaraVHanTFreebergM 2012 The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs. PLoS Genet 8 4 e1002617 doi:10.1371/journal.pgen.1002617
52. MontgomeryTARimY-SZhangCDowenRHPhillipsCM 2012 PIWI Associated siRNAs and piRNAs Specifically Require the Caenorhabditis elegans HEN1 Ortholog henn-1. PLoS Genet 8 4 e1002616 doi:10.1371/journal.pgen.1002616
53. Frokjaer-JensenCDavisMWHopkinsCENewmanBJThummelJM 2008 Single-copy insertion of transgenes in Caenorhabditis elegans. Nat Genet 40 1375 1383
54. MerrittCRasolosonDKoDSeydouxG 2008 3′ UTRs are the primary regulators of gene expression in the C. elegans germline. Curr Biol 18 1476 1482
55. KamathRSFraserAGDongYPoulinGDurbinR 2003 Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421 231 237
56. ZhangZBermanPMillerW 1998 Alignments without low-scoring regions. Journal of computational biology : a journal of computational molecular cell biology 5 197 210
57. FlicekPAmodeMRBarrellDBealKBrentS 2011 Ensembl 2011. Nucleic acids research 39 D800 806
58. CoxGNLauferJSKuschMEdgarRS 1980 Genetic and Phenotypic Characterization of Roller Mutants of CAENORHABDITIS ELEGANS. Genetics 95 317 339
59. KuschMEdgarRS 1986 Genetic studies of unusual loci that affect body shape of the nematode Caenorhabditis elegans and may code for cuticle structural proteins. Genetics 113 621 639
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