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DNA Repair of Eukaryotes Associated with Non-coding Small RNAs

  • Kang, Han-Chul (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Yoon, Sang-Hong (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Lee, Chang-Muk (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration) ;
  • Roh, Kyung Hee (Department of metabolic engineering, National Academy of Agricultural Science, Rural Development Administration)
  • Received : 2012.10.16
  • Accepted : 2012.11.26
  • Published : 2013.03.31

Abstract

In eukaryotes, most of the genome are transcribed, however only a small proportion of total transcripts encodes for protein, thus resulting in many of noncoding RNAs. In order to recover DNA damage including DNA double-strand breaks (DSBs) eukaryotes have evolved complex mechanisms and these are processed through coordinated mechanisms of protein sensors, transducers, and effectors including RNAs. During recent years, small RNAs have been increasingly studied and gradually considered as key regulators in various aspects of biology. Upon DNA damage, small RNAs including diRNAs (DSB induced RNA) are generated in both plant and human cell lines. Inhibition of their biogenesis has severe influence on DSB repair system.

Keywords

References

  1. Allinson SL, Dianova II, and Dianov GL (2003) Poly (ADP-ribose) polymerase in base excision repair: always engaged, but not essential for DNA damage processing. Acta Biochim Pol 50, 169-79.
  2. Autexier C and Lue NF (2006) The structure and function of telomerase reverse transcriptase. Annu Rev Biochem 75, 493-517. https://doi.org/10.1146/annurev.biochem.75.103004.142412
  3. Baltimore D (1985) Retroviruses and retrotransposons; the role of reverse transcription in shaping the eukaryotic genome. Cell 40, 481-2. https://doi.org/10.1016/0092-8674(85)90190-4
  4. Bartel DP (2004) microRNAs; genomics, biogenesis, mechanism and function. Cell 116, 281-97. https://doi.org/10.1016/S0092-8674(04)00045-5
  5. Baulcombe D (2004) RNA silencing in plants. Nature 431, 356-63. https://doi.org/10.1038/nature02874
  6. Caldecott KW (2008) Single-strand break repair and genetic disease. Nat Rev Gen 9, 619-31.
  7. Carthew RW and Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-55. https://doi.org/10.1016/j.cell.2009.01.035
  8. Chiu YL and Greene WC (2008) The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu Rev Immunol 26, 317-53. https://doi.org/10.1146/annurev.immunol.26.021607.090350
  9. Ciccia A and Elledge SJ (2010) The DNA damage response: making it safe to play with knives. Mol Cell 40, 179-204. https://doi.org/10.1016/j.molcel.2010.09.019
  10. Cortez D, Guntuku S, Qin J, and Elledge SJ (2001) ATR and ATRIP: partners in checkpoint signaling. Science 294, 1713-6. https://doi.org/10.1126/science.1065521
  11. Denli AM, Tops BB, Plasterk RH, Ketting RF, and Hannon GJ (2004) Processing of primary microRNAs by the microprocessor complex. Nature 432, 231-5. https://doi.org/10.1038/nature03049
  12. Fillingham J, Keogh MC, and Krogan NJ (2006) GammaH2Ax and its role in DNA double-strand break repair. Biochem Cell Biol 84, 568-77. https://doi.org/10.1139/o06-072
  13. Gregory RI, Yan KP, Amuthan G, and Clenfdrimada T (2004) The microprocessor complex mediates the genesis of microRNAs. Nature 432, 235-40. https://doi.org/10.1038/nature03120
  14. Han C, Wan G, Langley RR, Zhang X, and Lu X (2012) Crosstalk between the DNA damage response pathway and microRNAs. Cell Mol Life Sci 69, 2895-906. https://doi.org/10.1007/s00018-012-0959-8
  15. Hartlerrode AJ and Scully R (2009) Mechanisms of double-strand break repair in somatic mammalian cells. Biochem J 423,157-68. https://doi.org/10.1042/BJ20090942
  16. Helleday T (2010) Homologous recombination in cancer development, treatment and development of drug resistance. Carcinogenesis 31, 955-60. https://doi.org/10.1093/carcin/bgq064
  17. Helleday T, Lo J, and van Gent DC (2007) DNA double-strand break repair: From mechanistic understanding to cancer treatment. DNA Repair 6, 923-35. https://doi.org/10.1016/j.dnarep.2007.02.006
  18. Hendriks G, Calleja F, Besaratinaa A, Vrieling H, and Pfeifer GP (2010) Transcription-dependent cytosine deamination is a novel mechanism in ultraviolet light-induced mutagenesis. Curr Biol 20, 170-5. https://doi.org/10.1016/j.cub.2009.11.061
  19. Hoeijmakers JH (2001) Genome maintenance mechanism for preventing cancer. Nature 411, 366-74. https://doi.org/10.1038/35077232
  20. Huertas P and Aguilera A (2003) A cotranscriptionally formed DNA: RNA hybrids mediate transcription elongation impairmenr and transcriptionassociated recombination. Mol Cell 12, 711-21. https://doi.org/10.1016/j.molcel.2003.08.010
  21. Huertas P, Garcia-Rubio ML, Wellinger RE, Luna R, and Aguilera A (2006) An hpr1 point mutation that impairs transcription and mRNP biogenesis without increasing recombination. Mol Cell Biol 26,7451-65. https://doi.org/10.1128/MCB.00684-06
  22. Hutvagner G, Mclachlan J, and Pasquinelli AE (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834. https://doi.org/10.1126/science.1062961
  23. Hwang HW, Wentzel EA, and Mendell JT (2007) A hexanucleotide element directs microRNA nuclear import. Science 315, 97-100. https://doi.org/10.1126/science.1136235
  24. Kapranov P, Ozsolak F, Kim SW, and Foissac S (2010) New class of genetermini- associated human RNAs suggests a novel RNA copying mechanism. Nature 466, 642-6. https://doi.org/10.1038/nature09190
  25. Kasahara M, Clikeman JA, Bates DB, and Kogoma T (2000) Rec A proteindependent R-loop formation in vitro. Genes Dev 14, 360-5.
  26. Kasparek TR and Humphrey TC (2011) DNA double-strand break repair pathways, chromosomal rearrangements and cancer. Cell Develop Biol 22, 886-97. https://doi.org/10.1016/j.semcdb.2011.10.007
  27. Khobta A and Epe B (2012) Interactions between DNA damage, repair, and transcription. Mutat Res 736, 5-14. https://doi.org/10.1016/j.mrfmmm.2011.07.014
  28. Law JA and Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animnals. Nat Rev Genet 11, 204-20. https://doi.org/10.1038/nrg2719
  29. Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, Bamford DH et al. (2009) qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459, 274-7. https://doi.org/10.1038/nature08041
  30. Lee RC, Feinbaum RL, and Ambros V (1993) The C.elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin- 14. Cell 75, 843-54. https://doi.org/10.1016/0092-8674(93)90529-Y
  31. Lesage P and Todeschini A (2005) The life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res 110, 70-90. https://doi.org/10.1159/000084940
  32. Lieber MR (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79, 181-211. https://doi.org/10.1146/annurev.biochem.052308.093131
  33. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362, 709-15. https://doi.org/10.1038/362709a0
  34. 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, 1161-9. https://doi.org/10.1038/ncb2344
  35. Ma JB, YE K, and Patel DJ (2004) Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318-22. https://doi.org/10.1038/nature02519
  36. Ma JB, Yuan YR, Meister G, Pei Y, Tuschi T, and Patel DJ (2005) Structural basis for 5’end specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434, 666-70. https://doi.org/10.1038/nature03514
  37. Malone CD and Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136, 656-68. https://doi.org/10.1016/j.cell.2009.01.045
  38. Mochizuki K and Gorovsky M (2004) Conjugation specific small RNAs in Tetraherna have predicted properties of scan RNAs involved in genome rearrangement. Genes Dev 18, 2068-73. https://doi.org/10.1101/gad.1219904
  39. Moynahan ME and Jasin M (2010) Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat Rev Mol Cell Biol 11,196-207. https://doi.org/10.1038/nrm2851
  40. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, and Conklin DS (2002) Short hairpin RNAs induce sequence specific silencing in mammalian cells. Genes Dev 16, 948-58. https://doi.org/10.1101/gad.981002
  41. Paques F and Haber JE (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 63, 349-404.
  42. Paull TT, Rogakou Ep, Yamazaki V, Kirchgessner CU, Gellert M, and Bonner WM (2000) A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Curr Biol 10, 886-95. https://doi.org/10.1016/S0960-9822(00)00610-2
  43. Peng Y, Zhang H, Nagasawa R, Okayasu, HL, and Liber JS (2002) Silencing expression of the catalytic subunit of DNA-dependent protein kinase by small interfering RNA sensitizes human cells for radiation-induced chromosome damage, cell killing, and mutation. Cancer Res 62, 6400-4.
  44. Petermann E and Helledat T (2010) Pathways of mammalian replication fork restart. Nat Rev Mol Cell Biol 11, 683-7. https://doi.org/10.1038/nrm2974
  45. Polo SE and Jackson SP (2011) Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev 25, 409-33. https://doi.org/10.1101/gad.2021311
  46. Prado F and Aguilera A (2005) Impairment of replication fork progression mediates RNA pol III transcription-associated recombination. EMBO J 24, 1267−76. https://doi.org/10.1038/sj.emboj.7600602
  47. Rinn JL and Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81, 145-66. https://doi.org/10.1146/annurev-biochem-051410-092902
  48. Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ et al. (2005) Purified argonaute a2 and an siRNA from human RISC. Nat Struct Mol Biol 12, 340-9. https://doi.org/10.1038/nsmb918
  49. San-Filippo J, Sung P, and Klein H (2008) Mechanism of eukaryotic homologous recom-bination. Annu Rev Biochem 77, 229-57. https://doi.org/10.1146/annurev.biochem.77.061306.125255
  50. Sasaki M, Lange J, and Keeney S (2010) Genome destabilization by homologous recom-bination in the germ line. Nat Rev Mol Cell Biol 11, 182-95. https://doi.org/10.1038/nrm2849
  51. Singh SK, Roy S, and Choudhury SR (2010) DNA repair and recombination in higher plants. BMC Genomics 11, 443-51. https://doi.org/10.1186/1471-2164-11-443
  52. Soria G, Polo SE, and Almouzni G (2012) Prime, repair, restore; the active role of chromatin in the DNA damage response. Mol Cell 29, 723-34.
  53. Storici F, Bebenek K, Kunkel TA, Gordenin DA, and Resnick M (2007) RNA-templated DNA repair. Nature 447, 338-41. https://doi.org/10.1038/nature05720
  54. Strom CE, Johansson F, Uhlen M, Szigyarto CA, Erixon K, and Helleday T (2011) Poly (ADP-ribose) polymerase (PARP) is not involved in base excision repair but PARP inhibition traps a single-strand intermediate. Nucleic Acids Res 39, 3166-75. https://doi.org/10.1093/nar/gkq1241
  55. Su X, Chakravarti D, and Cho MS (2010) Tap63 suppresses metastasis through coordinate regulation of Dicer and miRNAs. Nature 467, 986-90. https://doi.org/10.1038/nature09459
  56. Teng SC, Kim B, and Gabriel A (1996) Retrotransposon reverse-transcriptase mediated repair of chromosomal breaks. Nature 383, 641-4. https://doi.org/10.1038/383641a0
  57. Toila NH and Joshua L (2007) Slicer and the argonautes. Nat Chem Biol 3, 36-43. https://doi.org/10.1038/nchembio848
  58. Tsai AG, Raghavan SC, Muschen M, and Hsieh CL (2008) Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell 135, 1130-42. https://doi.org/10.1016/j.cell.2008.10.035
  59. Yi R, Qin Y, Macara IG, and Culen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17, 3011V6. https://doi.org/10.1101/gad.1158803
  60. Wang B, Matsuoka S, Carpenter PB, and Elledge SJ (2002) 53BP1, a mediator of the DNA damage checkpoint. Science 298, 1435-8. https://doi.org/10.1126/science.1076182
  61. Wei W, Ba Z, Gao M, and Wu Y (2012) A role for small RNAs in DNA double-strand break repair. Cell 149, 101-12. https://doi.org/10.1016/j.cell.2012.03.002