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Tissue Expression Pattern of PMK-2 p38 MAPK Is Established by the miR-58 Family in
MicroRNAs are small, noncoding RNAs that act post-transcriptionally to inhibit expression of their target mRNAs. Gene expression studies of microRNAs and their target transcripts in diverse organisms have suggested that microRNAs may function to shape patterns of tissue expression. In this paper, we show that the miR-58/80-82 family of microRNAs, which accounts for roughly half of all C. elegans microRNAs at all developmental stages, defines the spatial expression pattern of PMK-2 p38 MAPK. While the pmk-2 gene is broadly transcribed, its tissue-specific expression is established by the redundant activities of miR-58, miR-80, miR-81, and miR-82, which switch off expression of PMK-2 through destabilization of pmk-2 mRNA in non-neuronal tissues. Our data suggest a housekeeping role for the miR-58/80-82 family in establishing and maintaining neuronal patterns of gene expression in C. elegans, and supports a more general role for microRNAs in establishing patterns of tissue expression.
Vyšlo v časopise: Tissue Expression Pattern of PMK-2 p38 MAPK Is Established by the miR-58 Family in. PLoS Genet 11(2): e32767. doi:10.1371/journal.pgen.1004997
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004997Souhrn
MicroRNAs are small, noncoding RNAs that act post-transcriptionally to inhibit expression of their target mRNAs. Gene expression studies of microRNAs and their target transcripts in diverse organisms have suggested that microRNAs may function to shape patterns of tissue expression. In this paper, we show that the miR-58/80-82 family of microRNAs, which accounts for roughly half of all C. elegans microRNAs at all developmental stages, defines the spatial expression pattern of PMK-2 p38 MAPK. While the pmk-2 gene is broadly transcribed, its tissue-specific expression is established by the redundant activities of miR-58, miR-80, miR-81, and miR-82, which switch off expression of PMK-2 through destabilization of pmk-2 mRNA in non-neuronal tissues. Our data suggest a housekeeping role for the miR-58/80-82 family in establishing and maintaining neuronal patterns of gene expression in C. elegans, and supports a more general role for microRNAs in establishing patterns of tissue expression.
Zdroje
1. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 : 843–854. 8252621
2. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403 : 901–906. 10706289
3. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans. Science 294 : 858–862. 11679671
4. Lee RC, Ambros V (2001) An Extensive Class of Small RNAs in Caenorhabditis elegans. Science 294 : 862–864. 11679672
5. Miska EA, Alvarez-Saavedra E, Abbott AL, Lau NC, Hellman AB, et al. (2007) Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3: e215. 18085825
6. Alvarez-Saavedra E, Horvitz HR (2010) Many Families of C. elegans MicroRNAs Are Not Essential for Development or Viability. Curr Biol 20 : 367–373. doi: 10.1016/j.cub.2009.12.051 20096582
7. Kato M, de Lencastre A, Pincus Z, Slack FJ (2009) Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol 10: R54. doi: 10.1186/gb-2009-10-5-r54 19460142
8. Isik M, Korswagen HC, Berezikov E (2010) Expression patterns of intronic microRNAs in Caenorhabditis elegans. Silence 1 : 5. doi: 10.1186/1758-907X-1-5 20226079
9. Jovanovic M, Reiter L, Clark A, Weiss M, Picotti P, et al. (2012) RIP-chip-SRM—a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Res 22 : 1360–1371. doi: 10.1101/gr.133330.111 22454234
10. Berman K, McKay J, Avery L, Cobb M (2001) Isolation and characterization of pmk-(1–3): three p38 homologs in Caenorhabditis elegans. Mol Cell Biol Res Commun MCBRC 4 : 337–344. 11703092
11. Kim DH, Feinbaum R, Alloing G, Emerson FE, Garsin DA, et al. (2002) A conserved p38 MAP kinase pathway in Caenorhabditis elegans innate immunity. Science 297 : 623–626. 12142542
12. Shivers RP, Kooistra T, Chu SW, Pagano DJ, Kim DH (2009) Tissue-specific activities of an immune signaling module regulate physiological responses to pathogenic and nutritional bacteria in C. elegans. Cell Host Microbe 6 : 321–330. doi: 10.1016/j.chom.2009.09.001 19837372
13. Liberati NT, Fitzgerald KA, Kim DH, Feinbaum R, Golenbock DT, et al. (2004) Requirement for a conserved Toll/interleukin-1 resistance domain protein in the Caenorhabditis elegans immune response. Proc Natl Acad Sci U S A 101 : 6593–6598. 15123841
14. Couillault C, Pujol N, Reboul J, Sabatier L, Guichou J-F, et al. (2004) TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM. Nat Immunol 5 : 488–494. 15048112
15. Chuang C-F, Bargmann CI (2005) A Toll-interleukin 1 repeat protein at the synapse specifies asymmetric odorant receptor expression via ASK1 MAPKKK signaling. Genes Dev 19 : 270–281. 15625192
16. Tanaka-Hino M, Sagasti A, Hisamoto N, Kawasaki M, Nakano S, et al. (2002) SEK-1 MAPKK mediates Ca2+ signaling to determine neuronal asymmetric development in Caenorhabditis elegans. EMBO Rep 3 : 56–62. 11751572
17. Sagasti A, Hisamoto N, Hyodo J, Tanaka-Hino M, Matsumoto K, et al. (2001) The CaMKII UNC-43 activates the MAPKKK NSY-1 to execute a lateral signaling decision required for asymmetric olfactory neuron fates. Cell 105 : 221–232. 11336672
18. Zhang Y, Lu H, Bargmann CI (2005) Pathogenic bacteria induce aversive olfactory learning in Caenorhabditis elegans. Nature 438 : 179–184. 16281027
19. Shivers RP, Pagano DJ, Kooistra T, Richardson CE, Reddy KC, et al. (2010) Phosphorylation of the conserved transcription factor ATF-7 by PMK-1 p38 MAPK regulates innate immunity in Caenorhabditis elegans. PLoS Genet 6: e1000892. doi: 10.1371/journal.pgen.1000892 20369020
20. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 : 15–20. 15652477
21. Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, et al. (2008) Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 18 : 2005–2015. doi: 10.1101/gr.083055.108 18981266
22. Ebert MS, Sharp PA (2012) Roles for MicroRNAs in Conferring Robustness to Biological Processes. Cell 149 : 515–524. doi: 10.1016/j.cell.2012.04.005 22541426
23. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM (2005) Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution. Cell 123 : 1133–1146. 16337999
24. Farh KK-H, Grimson A, Jan C, Lewis BP, Johnston WK, et al. (2005) The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution. Science 310 : 1817–1821. 16308420
25. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N (2006) Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A 103 : 2746–2751. 16477010
26. Shkumatava A, Stark A, Sive H, Bartel DP (2009) Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Dev 23 : 466–481. doi: 10.1101/gad.1745709 19240133
27. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, et al. (2009) Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev 23 : 619–632. doi: 10.1101/gad.1760209 19240126
28. Blumenthal T (2012) Trans-splicing and operons in C. elegans. WormBook Online Rev C Elegans Biol: 1–11.
29. Johnston RJ, Hobert O (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426 : 845–849. 14685240
30. Chang S, Johnston RJ, Frøkjaer-Jensen C, Lockery S, Hobert O (2004) MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430 : 785–789. 15306811
31. Yoo AS, Greenwald I (2005) LIN-12/Notch Activation Leads to MicroRNA-Mediated Down-Regulation of Vav in C. elegans. Science 310 : 1330–1333. 16239437
32. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 : 843–854. 8252621
33. Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, et al. (2011) A spatial and temporal map of C. elegans gene expression. Genome Res 21 : 325–341. doi: 10.1101/gr.114595.110 21177967
34. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, et al. (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol CB 12 : 735–739.
35. Brenner S (1974) The genetics of Caenorhabditis elegans. Genetics 77 : 71–94. 4366476
36. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, et al. (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9 : 676–682. doi: 10.1038/nmeth.2019 22743772
37. Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, et al. (2013) Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10 : 741–743. doi: 10.1038/nmeth.2532 23817069
38. Mello CC, Kramer JM, Stinchcomb D, Ambros V (1991) Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J 10 : 3959–3970. 1935914
39. Jorgensen EM, Mango SE (2002) The art and design of genetic screens: caenorhabditis elegans. Nat Rev Genet 3 : 356–369. 11988761
40. Wicks SR, Yeh RT, Gish WR, Waterston RH, Plasterk RH (2001) Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet 28 : 160–164. 11381264
41. Davis MW, Hammarlund M, Harrach T, Hullett P, Olsen S, et al. (2005) Rapid single nucleotide polymorphism mapping in C. elegans. BMC Genomics 6 : 118. 16156901
42. Friedman RC, Farh KK-H, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19 : 92–105. doi: 10.1101/gr.082701.108 18955434
43. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45. 11328886
44. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, et al. (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408 : 325–330. 11099033
45. Andersen EC (2011) PCR-directed in vivo plasmid construction using homologous recombination in baker’s yeast. Methods Mol Biol Clifton NJ 772 : 409–421. doi: 10.1007/978-1-61779-228-1_24 22065452
46. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15 : 1034–1050. 16024819
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