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PMID: 17526642 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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

RNA (New York, N.Y.) ·Vol. 13 ·No. 7 ·2007-07-00 ·Pages 1090-102

Welker NC, Habig JW, Bass BL

Abstract

We describe the first microarray analysis of a whole animal containing a mutation in the Dicer gene. We used adult Caenorhabditis elegans and, to distinguish among different roles of Dicer, we also performed microarray analyses of animals with mutations in rde-4 and rde-1, which are involved in silencing by siRNA, but not miRNA. Surprisingly, we find that the X chromosome is greatly enriched for genes regulated by Dicer. Comparison of all three microarray data sets indicates the majority of Dicer-regulated genes are not dependent on RDE-4 or RDE-1, including the X-linked genes. However, all three data sets are enriched in genes important for innate immunity and, specifically, show increased expression of innate immunity genes.

MeSH Terms
Animals Animals, Genetically Modified Caenorhabditis elegans/genetics Caenorhabditis elegans Proteins/genetics Gene Deletion Gene Expression Regulation Immunity, Innate/genetics MicroRNAs/genetics Oligonucleotide Array Sequence Analysis RNA, Small Interfering/genetics RNA-Binding Proteins/genetics Ribonuclease III/genetics,physiology X Chromosome/chemistry
Chemicals
Caenorhabditis elegans Proteins MicroRNAs RDE-4 protein, C elegans RNA, Small Interfering RNA-Binding Proteins rde-1 protein, C elegans Ribonuclease III
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Welker Noah C
Department of Biochemistry and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, 84112, USA.
Habig Jeffrey W
Bass Brenda L
References (52)
52 references, click to expand
  1. Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells.
    Nucleic Acids Res. 2006;34(17):4801-15 PMID: 16971455
  2. A conserved role for a GATA transcription factor in regulating epithelial innate immune responses.
    Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14086-91 PMID: 16968778
  3. 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
  4. p38 MAPK regulates expression of immune response genes and contributes to longevity in C. elegans.
    PLoS Genet. 2006 Nov 10;2(11):e183 PMID: 17096597
  5. 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
  6. GATA transcription factor required for immunity to bacterial and fungal pathogens.
    PLoS One. 2006;1:e77 PMID: 17183709
  7. Distinct populations of primary and secondary effectors during RNAi in C. elegans.
    Science. 2007 Jan 12;315(5809):241-4 PMID: 17124291
  8. Secondary siRNAs result from unprimed RNA synthesis and form a distinct class.
    Science. 2007 Jan 12;315(5809):244-7 PMID: 17158288
  9. The rde-1 gene, RNA interference, and transposon silencing in C. elegans.
    Cell. 1999 Oct 15;99(2):123-32 PMID: 10535731
  10. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans.
    Nature. 2000 Feb 24;403(6772):901-6 PMID: 10706289
  11. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  12. The Caenorhabditis elegans unc-32 gene encodes alternative forms of a vacuolar ATPase a subunit.
    J Biol Chem. 2001 Apr 13;276(15):11913-21 PMID: 11110798
  13. 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
  14. A reverse genetic analysis of components of the Toll signaling pathway in Caenorhabditis elegans.
    Curr Biol. 2001 Jun 5;11(11):809-21 PMID: 11516642
  15. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans.
    Science. 2001 Sep 21;293(5538):2269-71 PMID: 11486053
  16. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans.
    Genes Dev. 2001 Oct 15;15(20):2654-9 PMID: 11641272
  17. Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans.
    RNA. 2001 Oct;7(10):1397-402 PMID: 11680844
  18. Identification of novel genes coding for small expressed RNAs.
    Science. 2001 Oct 26;294(5543):853-8 PMID: 11679670
  19. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.
    Science. 2001 Oct 26;294(5543):858-62 PMID: 11679671
  20. An extensive class of small RNAs in Caenorhabditis elegans.
    Science. 2001 Oct 26;294(5543):862-4 PMID: 11679672
  21. 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
  22. Inducible antibacterial defense system in C. elegans.
    Curr Biol. 2002 Jul 23;12(14):1209-14 PMID: 12176330
  23. MicroRNAs and other tiny endogenous RNAs in C. elegans.
    Curr Biol. 2003 May 13;13(10):807-18 PMID: 12747828
  24. Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans.
    Development. 2004 Jan;131(2):311-23 PMID: 14668411
  25. TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM.
    Nat Immunol. 2004 May;5(5):488-94 PMID: 15048112
  26. Evolution of the innate immune system: the worm perspective.
    Immunol Rev. 2004 Apr;198:36-58 PMID: 15199953
  27. Mitogen-activated protein kinase pathways defend against bacterial pore-forming toxins.
    Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10995-1000 PMID: 15256590
  28. The genetics of Caenorhabditis elegans.
    Genetics. 1974 May;77(1):71-94 PMID: 4366476
  29. Analysis of the constancy of DNA sequences during development and evolution of the nematode Caenorhabditis elegans.
    Proc Natl Acad Sci U S A. 1979 Mar;76(3):1333-7 PMID: 286315
  30. RNAi-mediated pathways in the nucleus.
    Nat Rev Genet. 2005 Jan;6(1):24-35 PMID: 15630419
  31. Global effects on gene expression in fission yeast by silencing and RNA interference machineries.
    Mol Cell Biol. 2005 Jan;25(2):590-601 PMID: 15632061
  32. The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans.
    Dev Cell. 2005 Mar;8(3):321-30 PMID: 15737928
  33. Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee.
    Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):4063-7 PMID: 15728731
  34. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W460-4 PMID: 15980512
  35. Silence from within: endogenous siRNAs and miRNAs.
    Cell. 2005 Jul 15;122(1):9-12 PMID: 16009127
  36. RNA interference is an antiviral defence mechanism in Caenorhabditis elegans.
    Nature. 2005 Aug 18;436(7053):1044-7 PMID: 16107852
  37. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation.
    Cell. 2005 Aug 26;122(4):553-63 PMID: 16122423
  38. The yin and yang of type I interferon activity in bacterial infection.
    Nat Rev Immunol. 2005 Sep;5(9):675-87 PMID: 16110316
  39. EGO-1, a putative RNA-dependent RNA polymerase, is required for heterochromatin assembly on unpaired dna during C. elegans meiosis.
    Curr Biol. 2005 Nov 8;15(21):1972-8 PMID: 16271877
  40. An antiviral role for the RNA interference machinery in Caenorhabditis elegans.
    Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18420-4 PMID: 16339901
  41. Innate immune recognition of viral infection.
    Nat Immunol. 2006 Feb;7(2):131-7 PMID: 16424890
  42. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways.
    Cell. 2006 Jan 27;124(2):343-54 PMID: 16439208
  43. A genome-wide map of conserved microRNA targets in C. elegans.
    Curr Biol. 2006 Mar 7;16(5):460-71 PMID: 16458514
  44. Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans.
    RNA. 2006 Apr;12(4):589-97 PMID: 16489184
  45. RNA interference directs innate immunity against viruses in adult Drosophila.
    Science. 2006 Apr 21;312(5772):452-4 PMID: 16556799
  46. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling.
    Science. 2006 Apr 21;312(5772):436-9 PMID: 16627744
  47. RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA.
    RNA. 2006 May;12(5):807-18 PMID: 16603715
  48. Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses.
    Nature. 2006 May 4;441(7089):101-5 PMID: 16625202
  49. Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila.
    Nat Immunol. 2006 Jun;7(6):590-7 PMID: 16554838
  50. Intracellular pattern recognition receptors in the host response.
    Nature. 2006 Jul 6;442(7098):39-44 PMID: 16823444
  51. Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum.
    Genome Res. 2006 Aug;16(8):1005-16 PMID: 16809667
  52. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster.
    Genes Dev. 2006 Nov 1;20(21):2985-95 PMID: 17079687
Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1355-8382
DOI
10.1261/rna.542107
Published
2007-07-00
Epub
2007-00-25
Pages
1090-102
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC1894926
Subset
IM
Grants
NIGMS NIH HHS · R01 GM067106 · United States
NIGMS NIH HHS · R01 GM067106-03 · United States
NIGMS NIH HHS · GM067106 · United States
External Links
PubMed source DOI: 10.1261/rna.542107 PMC Full Text View journal details
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