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Vol. 143, No. 1-3, 2014
Issue release date: August 2014
Section title: Organization and Dynamics of Plant Chromatin
Cytogenet Genome Res 2014;143:51-59
(DOI:10.1159/000360774)

Drugs for Plant Chromosome and Chromatin Research

Pecinka A. · Liu C.-H.
Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany

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Article / Publication Details

First-Page Preview
Abstract of Organization and Dynamics of Plant Chromatin

Published online: 3/28/2014

Number of Print Pages: 9
Number of Figures: 1
Number of Tables: 2

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: http://www.karger.com/CGR

Abstract

Eukaryotic genomes are organized into chromosomes. Genetic information regularly becomes damaged and requires repair in order to ensure genome stability. Furthermore, expression of individual genetic elements on the chromosome(s) is controlled by several factors, including chromatin. Understanding the functions of chromatin may provide efficient tools for regulating gene expression. There has been great progress in understanding genome control using genetic mutations, but the use of mutants is sometimes not possible or may require additional interference with DNA or chromatin structure using specific treatments in order to obtain phenotypes. Therefore, chemical genetics has become an integral part of plant genome research. Here, we summarize information on the most commonly used drugs for chromatin and DNA damage repair studies, with the aim of simplifying the choice of drug and the estimation of possible side effects for current and future research.


Article / Publication Details

First-Page Preview
Abstract of Organization and Dynamics of Plant Chromatin

Published online: 3/28/2014

Number of Print Pages: 9
Number of Figures: 1
Number of Tables: 2

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: http://www.karger.com/CGR


Copyright / Drug Dosage

Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

References

  1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, et al: Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotech 30:174-178 (2012).
  2. Abe K, Osakabe K, Ishikawa Y, Tagiri A, Yamanouchi H, et al: Inefficient double-strand DNA break repair is associated with increased fasciation in Arabidopsis BRCA2 mutants. J Exp Bot 60:2751-2761 (2009).
  3. Adachi S, Minamisawa K, Okushima Y, Inagaki S, Yoshiyama K, et al: Programmed induction of endoreduplication by DNA double-strand breaks in Arabidopsis. Proc Natl Acad Sci USA 108:10004-10009 (2011).
  4. Arase S, Kasai M, Kanazawa A: In planta assays involving epigenetically silenced genes reveal inhibition of cytosine methylation by genistein. Plant Methods 8:10 (2012).
  5. Bagherieh-Najjar MB, de Vries OMH, Hille J, Dijkwel PP: Arabidopsis RecQl4A suppresses homologous recombination and modulates DNA damage responses. Plant J 43:789-798 (2005).
  6. Baubec T, Pecinka A, Rozhon W, Mittelsten Scheid O: Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine. Plant J 57:542-554 (2009).
  7. Baubec T, Dinh HQ, Pecinka A, Rakic B, Rozhon W, et al: Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic states in Arabidopsis. Plant Cell 22:34-47 (2010).
  8. Baubec T, Finke A, Mittelsten Scheid O, Pecinka A: Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Rep, Epub ahead of print (2014).
  9. Beranek DT: Distribution of methyl and ethyl adducts following alkylation with monofunctional alkylating agents. Mutat Res 231:11-30 (1990).
  10. Bleuyard JY, Gallego ME, Savigny F, White CI: Differing requirements for the Arabidopsis Rad51 paralogs in meiosis and DNA repair. Plant J 41:533-545 (2005).
  11. Bray CM, West CE: DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity. New Phytol 168:511-528 (2005).
  12. Britt AB: DNA damage and repair in plants. Annu Rev Plant Physiol Plant Mol Biol 47:75-100 (1996).
  13. Brueckner B, Garcia Boy R, Siedlecki P, Musch T, Kliem HC, et al: Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases. Cancer Res 65:6305-6311 (2005).
  14. Cappadocia L, Maréchal A, Parent JS, Lepage É, Sygusch J, Brisson N: Crystal structures of DNA-whirly complexes and their role in Arabidopsis organelle genome repair. Plant Cell 22:1849-1867 (2010).
  15. Champion C, Guianvarc'h D, Sénamaud-Beaufort C, Jurkowska RZ, Jeltsch A, et al: Mechanistic insights on the inhibition of C5 DNA methyltransferases by zebularine. PLoS One 5:e12388 (2010).
  16. Chang S, Pikaard CS: Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation. J Biol Chem 280:796-804 (2005).
  17. Christopherson RI, Lyons SD, Wilson PK: Inhibitors of de novo nucleotide biosynthesis as drugs. Acc Chem Res 35:961-971 (2002).
  18. Cook GS, Grønlund AL, Siciliano I, Spadafora N, Amini M, et al: Plant WEE1 kinase is cell cycle regulated and removed at mitosis via the 26S proteasome machinery. J Exp Bot 64:2093-2106 (2013).
  19. Cools T, Iantcheva A, Maes S, Van den Daele H, De Veylder L: A replication stress-induced synchronization method for Arabidopsis thaliana root meristems. Plant J 64:705-714 (2010).
  20. Cools T, Iantcheva A, Weimer AK, Boens S, Takahashi N, et al: The Arabidopsis thaliana checkpoint kinase WEE1 protects against premature vascular differentiation during replication stress. Plant Cell 23:1435-1448 (2011).
  21. Cooper J, Henikoff S, Comai L, Till B: TILLING and ecotilling for rice, in Yang Y (ed): Rice Protocols, pp 39-56 (Humana Press, New York 2013).
  22. Cox R, Irving CC: Inhibition of DNA methylation by S-adenosylethionine with the production of methyl-deficient DNA in regenerating rat liver. Cancer Res 37:222-225 (1977).

    External Resources

  23. Culligan K, Tissier A, Britt A: ATR regulates a G2-phase cell-cycle checkpoint in Arabidopsis thaliana. Plant Cell 16:1091-1104 (2004).
  24. Dai X, Hayashi K, Nozaki H, Cheng Y, Zhao Y: Genetic and chemical analyses of the action mechanisms of sirtinol in Arabidopsis. Proc Natl Acad Sci USA 102:3129-3134 (2005).
  25. Da Ines O, Degroote F, Goubely C, Amiard S, Gallego ME, White CI: Meiotic recombination in Arabidopsis is catalysed by DMC1, with RAD51 playing a supporting role. PLoS Genet 9:e1003787 (2013).
  26. Deans AJ, West SC: DNA interstrand crosslink repair and cancer. Nat Rev Cancer 11:467-480 (2011).
  27. De Schutter K, Joubès J, Cools T, Verkest A, Corellou F, et al: Arabidopsis WEE1 kinase controls cell cycle arrest in response to activation of the DNA integrity checkpoint. Plant Cell 19:211-225 (2007).
  28. Fajkus J, Vyskot B, Bezděk M: Changes in chromatin structure due to hypomethylation induced with 5-azacytidine or DL-ethionine. FEBS Lett 314:13-16 (1992).
  29. Feng S, Jacobsen SE, Reik W: Epigenetic reprogramming in plant and animal development. Science 330:622-627 (2010).
  30. Foerster AM, Dinh HQ, Sedman L, Wohlrab B, Mittelsten Scheid O: Genetic rearrangements can modify chromatin features at epialleles. PLoS Genet 7:e1002331 (2011).
  31. Francis D: A commentary on the G2/M transition of the plant cell cycle. Ann Bot 107:1065-1070 (2011).
  32. Fu D, Calvo JA, Samson LD: Balancing repair and tolerance of DNA damage caused by alkylating agents. Nat Rev Cancer 12:104-120 (2012).
  33. Gendler K, Paulsen T, Napoli C: ChromDB: the chromatin database. Nucleic Acids Res 36:D298-D302 (2008).
  34. Gichner T: Differential genotoxicity of ethyl methanesulphonate, N-ethyl-N-nitrosourea and maleic hydrazide in tobacco seedlings based on data of the Comet assay and two recombination assays. Mutat Res 538:171-179 (2003).
  35. Grigaravičius P, Rapp A, Greulich KO: A direct view by immunofluorescent comet assay (IFCA) of DNA damage induced by nicking and cutting enzymes, ionizing 137Cs radiation, UV-A laser microbeam irradiation and the radiomimetic drug bleomycin. Mutagenesis 24:191-197 (2009).
  36. Grozinger CM, Chao ED, Blackwell HE, Moazed D, Schreiber SL: Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J Biol Chem 276:38837-38843 (2001).
  37. Haag JR, Pikaard CS: Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 12:483-492 (2011).
  38. Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, et al: In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol Cell 48:811-818 (2012).
  39. Hartwig B, James GV, Konrad K, Schneeberger K, Turck F: Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks. Plant Physiol 160:591-600 (2012).
  40. Hollender C, Liu Z: Histone deacetylase genes in Arabidopsis development. J Integrat Plant Biol 50:875-885 (2008).
  41. Houser S, Koshlatyi S, Lu T, Gopen T, Bargonetti J: Camptothecin and zeocin can increase p53 levels during all cell cycle stages. Biochem Biophys Res Commun 289:998-1009 (2001).
  42. Huang L, Sun Q, Qin F, Li C, Zhao Y, et al: Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol 144:1508-1519 (2007).
  43. Jamieson ER, Lippard SJ: Structure, recognition, and processing of cisplatin-DNA adducts. Chem Rev 99:2467-2498 (1999).
  44. Juul T, Malolepszy A, Dybkær K, Kidmose R, Rasmussen JT, et al: The in vivo toxicity of hydroxyurea depends on its direct target catalase. J Biol Chem 285:21411-21415 (2010).
  45. Kim Y: Analysis of gene expression upon DNA damage in Arabidopsis. J Plant Biol 49:298-302 (2006).

    External Resources

  46. Kim Y, Schumaker K, Zhu J-K: EMS mutagenesis of Arabidopsis, in Salinas J, Sanchez-Serrano JJ (eds): Arabidopsis Protocols, pp 101-103 (Humana Press, Totowa 2006).
  47. Koukalová B, Votruba I, Fojtová M, Holý A, Kovaŕík A: Hypomethylation of CNG targets induced with dihydroxypropyladenine is rapidly reversed in the course of mitotic cell division in tobacco. Theor Appl Genet 105:796-801 (2002).
  48. Kovařík A, Van Houdt H, Holý A, Depicker A: Drug-induced hypomethylation of a posttranscriptionally silenced transgene locus of tobacco leads to partial release of silencing. FEBS Lett 467:47-51 (2000).
  49. Lang J, Smetana O, Sanchez-Calderon L, Lincker F, Genestier J, et al: Plant γH2AX foci are required for proper DNA DSB repair responses and colocalize with E2F factors. New Phytol 194:353-363 (2012).
  50. Liang L, Flury S, Kalck V, Hohn B, Molinier J: CENTRIN2 interacts with the Arabidopsis homolog of the human XPC protein (AtRAD4) and contributes to efficient synthesis-dependent repair of bulky DNA lesions. Plant Mol Biol 61:345-356 (2006).
  51. Lundin C, North M, Erixon K, Walters K, Jenssen D, et al: Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks. Nucleic Acids Res 33:3799-3811 (2005).
  52. Ma Q, Akiyama Y, Xu Z, Konishi K, Hecht SM: Identification and cleavage site analysis of DNA sequences bound strongly by bleomycin. J Am Chem Soc 131:2013-2022 (2009).
  53. Majerová E, Fojtová M, Mozgová I, Bittová M, Fajkus J: Hypomethylating drugs efficiently decrease cytosine methylation in telomeric DNA and activate telomerase without affecting telomere lengths in tobacco cells. Plant Mol Biol 77:371-380 (2011).
  54. Mannuss A, Dukowic-Schulze S, Suer S, Hartung F, Pacher M, Puchta H: RAD5A, RECQ4A, and MUS81 have specific functions in homologous recombination and define different pathways of DNA repair in Arabidopsis thaliana. Plant Cell 22:3318-3330 (2010).
  55. Mathieu O, Reinders J, Čaikovski M, Smathajitt C, Paszkowski J: Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130:851-862 (2007).
  56. Mills WR, Reeves M, Fowler DL, Capo SF: DNA synthesis in chloroplasts: III. The DNA gyrase inhibitors nalidixic acid and novobiocin inhibit both thymidine incorporation into DNA and photosynthetic oxygen evolution by isolated chloroplasts. J Exp Bot 40:425-429 (1989).

    External Resources

  57. Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T: Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212-214 (2001).
  58. Narsai R, Howell KA, Millar AH, O'Toole N, Small I, Whelan J: Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell 19:3418-3436 (2007).
  59. Nezames CD, Sjogren CA, Barajas JF, Larsen PB: The Arabidopsis cell cycle checkpoint regulators TANMEI/ALT2 and ATR mediate the active process of aluminum-dependent root growth inhibition. Plant Cell 24:608-621 (2012).
  60. Nolan PM, Hugill A, Cox RD: ENU mutagenesis in the mouse: application to human genetic disease. Brief Funct Genomic Proteomic 1:278-289 (2002).
  61. Nordstrom KJV, Albani MC, James GV, Gutjahr C, Hartwig B, et al: Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nat Biotechnol 31:325-330 (2013).
  62. Osakabe K, Abe K, Yoshioka T, Osakabe Y, Todoriki S, et al: Isolation and characterization of the RAD54 gene from Arabidopsis thaliana. Plant J 48:827-842 (2006).
  63. Pan WH, Houben A, Schlegel R: Highly effective cell synchronization in plant roots by hydroxyurea and amiprophos-methyl or colchicine. Genome 36:387-390 (1993).
  64. Pecinka A, Rosa M, Schikora A, Berlinger M, Hirt H, et al: Transgenerational stress memory is not a general response in Arabidopsis. PLoS One 4:e5202 (2009).
  65. Povirk LF: DNA damage and mutagenesis by radiomimetic DNA-cleaving agents: bleomycin, neocarzinostatin and other enediynes. Mutat Res 355:71-89 (1996).
  66. Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, et al: Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16:1021-1034 (2004).
  67. Roa H, Lang J, Culligan KM, Keller M, Holec S, et al: Ribonucleotide reductase regulation in response to genotoxic stress in Arabidopsis. Plant Physiol 151:461-471 (2009).
  68. Sega GA: A review of the genetic effects of ethyl methanesulfonate. Mutat Res 134:113-142 (1984).
  69. Shibuya T, Morimoto K: A review of the genotoxicity of 1-ethyl-1-nitrosourea. Mutat Res 297:3-38 (1993).
  70. Siddik ZH: Cisplatin: mode of cytotoxic action and molecular basis of resistance. Oncogene 22:7265-7279 (2003).
  71. Spadafora ND, Doonan JH, Herbert RJ, Bitonti MB, Wallace E, et al: Arabidopsis T-DNA insertional lines for CDC25 are hypersensitive to hydroxyurea but not to zeocin or salt stress. Ann Bot 107:1183-1192 (2011).
  72. Spadari S, Sala F, Pedrali-Noy G: Aphidicolin: a specific inhibitor of nuclear DNA replication in eukaryotes. Trends Biochem Sci 7:29-32 (1982).

    External Resources

  73. Srivastava VK, Busbee DL: Replicative enzymes, DNA polymerase alpha (pol α), and in vitro ageing. Exp Geront 38:1285-1297 (2003).
  74. Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE: Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152:352-364 (2013).
  75. Tanaka M, Kikuchi A, Kamada H: The Arabidopsis histone deacetylases HDA6 and HDA19 contribute to the repression of embryonic properties after germination. Plant Physiol 146:149-161 (2008).
  76. Tomasz M: Mitomycin C: small, fast and deadly (but very selective). Chem Biol 2:575-579 (1995).
  77. Wall MK, Mitchenall LA, Maxwell A: Arabidopsis thaliana DNA gyrase is targeted to chloroplasts and mitochondria. Proc Natl Acad Sci USA 101:7821-7826 (2004).
  78. Xu CR, Liu C, Wang YL, Li LC, Chen WQ, et al: Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis. Proc Natl Acad Sci USA 102:14469-14474 (2005).
  79. Yin H, Zhang X, Liu J, Wang Y, He J, et al: Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase ε mutation in Arabidopsis. Plant Cell 21:386-402 (2009).
  80. Zhang H, Deng X, Miki D, Cutler S, La H, et al: Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis. Plant Cell 24:1230-1241 (2012).
  81. Zhao Y, Dai X, Blackwell HE, Schreiber SL, Chory J: SIR1, an upstream component in auxin signaling identified by chemical genetics. Science 301:1107-1110 (2003).
  82. Zhong S, Fei Z, Chen YR, Zheng Y, Huang M, et al: Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31:154-159 (2013).