A small RNA response at DNA ends in Drosophila

Nucleic Acids Research

Volumn 40, Issue 19, 2012, Pages 9596-9603

  Michalik, Katharina M ^a,b   Böttcher, Romy ^a   Förstemann, Klaus ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOUBLE STRANDED RNA; PLASMID DNA; RNA PRECURSOR;

3' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DNA CLEAVAGE; DNA STRAND BREAKAGE; DROSOPHILA; ENZYME ACTIVITY; EXPRESSION VECTOR; FLOW CYTOMETRY; GENE CASSETTE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE REPRESSION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA ISOLATION; RNA SYNTHESIS; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION;

ANIMALS; CELLS, CULTURED; DNA; DNA BREAKS, DOUBLE-STRANDED; DNA BREAKS, SINGLE-STRANDED; DNA REPAIR; DROSOPHILA; RNA INTERFERENCE; RNA, SMALL INTERFERING; TRANSCRIPTION, GENETIC;

ARABIDOPSIS; VERTEBRATA;

EID: 84868091999     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks711     Document Type: Article

References (39)

1. Wyman, C. and Kanaar, R. (2006) DNA double-strand break repair: all's well that ends well. Annu. Rev. Genet., 40, 363-383. (Pubitemid 44956790)
2. Bartek, J. and Lukas, J. (2007) DNA damage checkpoints: from initiation to recovery or adaptation. Curr. Opin. Cell Biol., 19, 238-245. (Pubitemid 46386406)
3. Lukas, J., Lukas, C. and Bartek, J. (2011) More than just a focus: the chromatin response to DNA damage and its role in genome integrity maintenance. Nat. Cell Biol., 13, 1161-1169.
4. Aravin, A.A., Hannon, G.J. and Brennecke, J. (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science, 318, 761-764. (Pubitemid 351411762)
5. Wang, S.H. and Elgin, S.C. (2011) Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line. Proc. Natl Acad. Sci. USA, 108, 21164-21169.
6. Aravin, A.A. and Bourc'his, D. (2008) Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev., 22, 970-975. (Pubitemid 351544235)
7. Malone, C.D. and Hannon, G.J. (2009) Small RNAs as guardians of the genome. Cell, 136, 656-668.
8. Kawamura, Y., Saito, K., Kin, T., Ono, Y., Asai, K., Sunohara, T., Okada, T.N., Siomi, M.C. and Siomi, H. (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature, 453, 793-797. (Pubitemid 351793781)
9. Czech, B., Malone, C.D., Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, J.A., Sachidanandam, R. et al. (2008) An endogenous small interfering RNA pathway in Drosophila. Nature, 453, 798-802. (Pubitemid 351793787)
10. Okamura, K., Chung, W.J., Ruby, J.G., Guo, H., Bartel, D.P. and Lai, E.C. (2008) The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature, 453, 803-806. (Pubitemid 351793790)
11. Ghildiyal, M., Seitz, H., Horwich, M.D., Li, C., Du, T., Lee, S., Xu, J., Kittler, E.L., Zapp, M.L., Weng, Z. et al. (2008) Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science, 320, 1077-1081. (Pubitemid 351929549)
12. Francia, S., Michelini, F., Saxena, A., Tang, D., de Hoon, M., Anelli, V., Mione, M., Carnici, P. and d'Adda di Fagagna, F. (2012) Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature, 488, 231-235.
13. Wei, W., Ba, Z., Gao, M., Wu, Y., Ma, Y., Amiard, S., White, C.I., Danielsen, J.M., Yang, Y.G. and Qi, Y. (2012) A role for small RNAs in DNA double-strand break repair. Cell, 149, 101-112.
14. Hartig, J.V., Esslinger, S., Bottcher, R., Saito, K. and Forstemann, K. (2009) Endo-siRNAs depend on a new isoform of loquacious and target artificially introduced, high-copy sequences. EMBO J., 28, 2932-2944.
15. Forstemann, K., Horwich, M.D., Wee, L., Tomari, Y. and Zamore, P.D. (2007) Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell, 130, 287-297. (Pubitemid 47086327)
16. Hartig, J.V. and Forstemann, K. (2011) Loqs-PD and R2D2 define independent pathways for RISC generation in Drosophila. Nucleic Acids Res., 39, 3836-3851.
17. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
18. Bahmed, K., Seth, A., Nitiss, K.C. and Nitiss, J.L. (2011) End-processing during non-homologous end-joining: a role for exonuclease 1. Nucleic Acids Res., 39, 970-978.
19. Zhou, R., Czech, B., Brennecke, J., Sachidanandam, R., Wohlschlegel, J.A., Perrimon, N. and Hannon, G.J. (2009) Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA, 15, 1886-1895.
20. Lee, H.C., Chang, S.S., Choudhary, S., Aalto, A.P., Maiti, M., Bamford, D.H. and Liu, Y. (2009) qiRNA is a new type of small interfering RNA induced by DNA damage. Nature, 459, 274-277.
21. Lee, H.C., Aalto, A.P., Yang, Q., Chang, S.S., Huang, G., Fisher, D., Cha, J., Poranen, M.M., Bamford, D.H. and Liu, Y. (2010) The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and dsRNA for RNAi in a process requiring replication protein A and a DNA helicase. PLoS Biol., 8, e1000496.
22. Rieckmann, T., Kriegs, M., Nitsch, L., Hoffer, K., Rohaly, G., Kocher, S., Petersen, C., Dikomey, E., Dornreiter, I. and Dahm-Daphi, J. (2012) p53 modulates homologous recombination at I-SceI-induced double-strand breaks through cell-cycle regulation. Oncogene, April 9 (doi:10.1038/onc.2012.123; epub ahead of print).
23. Bi, X., Wei, S.C. and Rong, Y.S. (2004) Telomere protection without a telomerase; the role of ATM and Mre11 in Drosophila telomere maintenance. Curr. Biol., 14, 1348-1353. (Pubitemid 39081636)
24. Song, Y.H., Mirey, G., Betson, M., Haber, D.A. and Settleman, J. (2004) The Drosophila ATM ortholog, dATM, mediates the response to ionizing radiation and to spontaneous DNA damage during development. Curr. Biol., 14, 1354-1359. (Pubitemid 39081637)
25. Gonzalez-Reyes, A., Elliott, H. and St Johnston, D. (1997) Oocyte determination and the origin of polarity in Drosophila: the role of the spindle genes. Development, 124, 4927-4937. (Pubitemid 28025119)
26. Kondo, S. and Perrimon, N. (2011) A genome-wide RNAi screen identifies core components of the G-M DNA damage checkpoint. Sci. Signal., 4, rs1.
27. Kennerdell, J.R., Yamaguchi, S. and Carthew, R.W. (2002) RNAi is activated during Drosophila oocyte maturation in a manner dependent on aubergine and spindle-E. Genes Dev., 16, 1884-1889. (Pubitemid 34832918)
28. Dietzl, G., Chen, D., Schnorrer, F., Su, K.C., Barinova, Y., Fellner, M., Gasser, B., Kinsey, K., Oppel, S., Scheiblauer, S. et al. (2007) A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature, 448, 151-156. (Pubitemid 47067374)
29. Handler, D., Olivieri, D., Novatchkova, M., Gruber, F.S., Meixner, K., Mechtler, K., Stark, A., Sachidanandam, R. and Brennecke, J. (2011) A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J., 30, 3977-3993.
30. Haley, B., Foys, B. and Levine, M. (2010) Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila. Proc. Natl Acad. Sci. USA, 107, 11435-11440.
31. Haley, B., Hendrix, D., Trang, V. and Levine, M. (2008) A simplified miRNA-based gene silencing method for Drosophila melanogaster. Dev. Biol., 321, 482-490.
32. Ni, J.Q., Zhou, R., Czech, B., Liu, L.P., Holderbaum, L., Yang-Zhou, D., Shim, H.S., Tao, R., Handler, D., Karpowicz, P. et al. (2011) A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat. Methods, 8, 405-407.
33. Deshpande, G., Calhoun, G. and Schedl, P. (2005) Drosophila argonaute-2 is required early in embryogenesis for the assembly of centric/centromeric heterochromatin, nuclear division, nuclear migration, and germ-cell formation. Genes Dev., 19, 1680-1685. (Pubitemid 41058363)
34. Peng, J.C. and Karpen, G.H. (2007) H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nat. Cell Biol., 9, 25-35. (Pubitemid 46024194)
35. Moshkovich, N. and Lei, E.P. (2010) HP1 recruitment in the absence of argonaute proteins in Drosophila. PLoS Genet., 6, e1000880.
36. Cernilogar, F.M., Onorati, M.C., Kothe, G.O., Burroughs, A.M., Parsi, K.M., Breiling, A., Lo Sardo, F., Saxena, A., Miyoshi, K., Siomi, H. et al. (2011) Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature, 480, 391-395.
37. Khurana, J.S., Xu, J., Weng, Z. and Theurkauf, W.E. (2010) Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. PLoS Genet., 6, e1001246.
38. Haag, J.R. and Pikaard, C.S. (2011) Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol., 12, 483-492.
39. Svejstrup, J.Q. (2010) The interface between transcription and mechanisms maintaining genome integrity. Trends Biochem. Sci., 35, 333-338.