Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus

Journal of Genetics

Volumn 92, Issue 3, 2013, Pages 499-511

  Kumari, Renu ^a,c   Yadav, Gitanjali ^a   Sharma, Vishakha ^a,b   Sharma, Vinay ^c   Kumar, Sushil ^a,b  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

^b SKA Institution for Research Education and Development (SKAIRED)   (India)

^c BANASTHALI UNIVERSITY   (India)

Author keywords

18S rDNA; 5S rDNA; bisulphite sequencing; CMT3; demethylation; DNA demethylases; DNA methyl transferases; excision repair; mutagenic hot spots; phylogenetic relationships; RdDM; spontaneous mutagenesis

Indexed keywords

CATHARANTHUS ROSEUS;

CYTOSINE; RNA 18S; RNA 5S;

ARTICLE; CATHARANTHUS; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENE; PLEIOTROPY; SALT TOLERANCE;

BASE SEQUENCE; CATHARANTHUS; CPG ISLANDS; CYTOSINE; DNA METHYLATION; GENES, PLANT; GENETIC PLEIOTROPY; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 5S; SALT-TOLERANCE; SEQUENCE ANALYSIS, DNA;

EID: 84899574638     PISSN: 00221333     EISSN: 09737731     Source Type: Journal    
DOI: 10.1007/s12041-013-0300-9     Document Type: Article

References (60)

1. Agius F., Kapoor A. and Zhu J. K. 2006 Role of the Arabidopsis DNA glycosylases/lyase ROS1 in active DNA demethylation. Proc. Natl. Acad. Sci. USA103, 11796-11801.
2. Bennetzen J. L. and Zhu J. K. 2011 Epigenetics of the epigenome. Curr. Opin. Plant Biol. 14, 113-115.
3. Bhutani N., Burns D. M. and Blau H. M. 2011 DNA demethylation dynamics. Cell146, 866-872.
4. Blevins T., Pontes O., Pikaard C. S. and Meins Jr F. 2009 Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis. PLoS One4, e5932.
5. Cao X. and Jacobsen S. E. 2002 Role of the ArabidopsisDRM methyltransferase in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138-1144.
6. Carr I. M., Valleley E. M. A., Cordery S. F., Markham A. F. and Bonthron D. T. 2007 Sequence analysis and editing for bisulphite genomic sequencing projects. Nucleic Acids Res. 35, e79.
7. Chan S. W., Henderson I. R., Zhang X., Shah G., Chien J. S. and Jacobsen S. E. 2006 RNAi, DRD1 and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLos. Genet. 2, e83.
8. Chaudhary S., Sharma V., Prasad M., Bhatia S., Tripathi B. N., Yadav G. and Kumar S. 2011 Characterization and genetic linkage mapping of the horticulturally important mutation leafless inflorescence (lli) in periwinkle Catharanthus roseus. Sci. Hort. 129, 142-153.
9. Chaudhary S., Pandey R., Sharma V., Tripathi B. N. and Kumar S. 2013 Detection and mapping of QTLs affecting contents of pharmaceutical alkaloids in leaf and root of Catharanthus roseus. Agric. Res. 2, 9-23.
10. Choi S. H., Byun H., Kwan J. M., Issa J. J. and Yang A. S. 2007 Hydroxycarbamide in combination with azacitidine or decitabine is antagonistic on DNA methylation inhibition. Br. J. Haematol. 138, 616-623.
11. Choi Y., Gehring M., Johnson L., Hannon M., Harada J. J., Goldberg R. B. et al. 2002 DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell110, 33-42.
12. Dowen R. H., Pelizzola M., Schmitz R. J., Lister R., Dowen J. M., Nery J. R. et al. 2012 Widespread dynamic DNA methylation in response to biotic stress. Proc. Natl. Acad. Sci. USA109, 2183-2191.
13. Felsenstein J. 1989 PHYLIP - phylogeny inference package (version 3. 2). Cladistics5, 164-166.
14. Finnegan E. J. 1996 The role of DNA methylation in plant development. In Epigenetic mechanisms of gene regulation (ed. V. E. A. Russo, R. A. Martienssen and A. D. Riggs), pp. 127-140. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA.
15. Fulnecek J., Matyásek R. and Kovarík A. 2002 Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale. Mol. Genet. Genomics268, 510-517.
16. Garcia S., Crhák Khaitová L. and Kovařík A. 2012 Expression of 5S rRNA genes linked to 35S rDNA in plants, their epigenetic modification and regulatory element divergence. BMC Plant Biol. 12, 95.
17. Garcia-Aguilar M., Michand C., Leblanc O. and Grimanelli D. 2010 Inactivation of a DNA methylation pathway in maize reproductive organs results in apomixis-like phenotypes. Plant Cell22, 3249-3667.
18. Gong Z., Morales-Ruiz T., Ariza R. R., Roldan-Arjona T., David L. and Zhu J. K. 2002 ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell111, 803-814.
19. He G., Elling A. A. and Deng X. W. 2011 The epigenome and plant development. Annu. Rev. Plant Biol. 62, 411-435.
20. Huen M. S., Sy S. M., van Deursen J. M. and Chen J. 2008 Direct interaction between SET8 and proliferating cell nuclear antigen couples H4-K20 methylation with DNA replication. J. Biol. Chem. 283, 11073-11077.
21. Huson D. H. and Scornavacca C. 2012 Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061-1067.
22. Jackson S. P. and Bartek J. 2009 The DNA-damage response in human biology and disease. Nature461, 1071-1078.
23. Johannes F., Porcher E., Teixeira F. K., Saliba-Colombani V., Simon M., Agier N. et al. 2009 Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet. 5, e1000530.
24. Kankel M. W., Rasey D. E., Stoke T. L., Flowers S. K., Haag J. R., Jeddeloh J. A. et al. 2003 MET1 cytosine methyltransferase mutants. Genetics163, 1109-1122.
25. Karan R., DeLeon T., Biradar H. and Subudhi P. K. 2012 Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS One7, e40203.
26. Kulkarni R. N., Baskaran K., Chandrashekhara R. S. and Kumar S. 1999 Inheritance of morphological traits of periwinkle mutants with modified contents and yields of leaf and root alkaloids. Plant Breed. 118, 71-74.
27. Kulkarni R. N., Baskaran K., Chandrashekara R. S., Khanuja S. P. S., Darokar M. P., Shasany A. K. et al. 2003 'Dhawal', a high alkaloid producing periwinkle plant. US Patent No. 6, 548, 746.
28. Kumar S., Rai S. P., Rai S. K., Singh D. V., Srivastava S. and Mishra R. K. 2007 Plant variety of Catharanthus roseus named 'lli'. US Patent PP18315.
29. Kumar S., Chaudhary S., Kumari R., Sharma V. and Kumar A. 2012 Development of improved horticultural genotypes characterized by novel over-flowering inflorescence trait in periwinkle, Catharanthus roseus. Proc. Natl. Acad. Sci. India Sect. B82, 399-404.
30. Kumar S., Kumari R., Sharma V. and Sharma V. 2013 Roles and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants. J. Genet. doi: 10. 1007/s12041-013-0273-8.
31. Kumari R., Chaudhary S., Mishra R. K., Rai S. P., Rai S. K., Sharma V. et al. 2010 Regulation of lifespan by the LLI and EGD genes in the perennial plant species, Catharanthus roseus. Proc. Indian Natl. Sci. Acad. 76, 27-39.
32. Kumari R., Sharma V., Sharma V. and Kumar S. 2013 Pleiotropic phenotypes of the salt tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance. J. Genet. doi: 10. 1007/s12041-013-0271-x.
33. Li L. C. and Dahiya R. 2002 MethPrimer: designing primers for methylation PCRs. Bioinformatics18, 1427-1431.
34. Lindroth A. M., Cao X., Jackson J. P., Zilberman D., McCallum C. M., Henikoff S. and Jacobsen S. E. 2001 Requirement of CHROMOMETHYLASE 3 for maintenance of CpXpG methylation. Science202, 2077-2080.
35. Lira-Medeiros C. F., Parisod C., Fernandes R. A., Mata C. S., Cardosa M. A. and Ferreira P. C. 2010 Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One5, e10326.
36. Luna E., Bruce T. J., Roberts M. R., Flors V. and Ton J. 2012 Next-generation systemic acquired resistance. Plant Physiol. 158, 844-853.
37. Mathieu O., Yukawa Y., Prieto J., Vaillant I., Sugiura M. and Tourmente S. 2003 Identification and characterization of transcription factor III A and ribosomal protein L5 from Arabidopsis thaliana. Nucleic Acids Res. 31, 2424-2433.
38. Mazin A. L. 1993 The mechanism of replicative and post-replicative DNA methylation as a generator of mutations in a cell. Mol. Biol. (Mosk) 27, 965-979.
39. Mishra P., Uniyal G. C., Sharma S. and Kumar S. 2001 Pattern of diversity for morphological and yield related traits among the periwinkle Catharanthus roseus accessions collected from in and around Indian subcontinent. Genet. Res. Crop Evol. 48, 273-286.
40. Ortega-Galisteo A. P., Morales-Ruiz T., Ariza R. R. and Roldan-Arjona T. 2008 Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol. Biol. 67, 671-681.
41. Pfeifer G. P. 2006 Mutagenesis at methylated CpG sequences. CTMI301, 259-281.
42. Rai S. P., Luthra R. and Kumar S. 2003 Salt-tolerant mutants in glycophytic salinity response (GSR) genes in Catharanthus roseus. Theor. Appl. Genet. 106, 221-230.
43. Ream T. S., Haag J. R., Wierzbicki A. T., Nicora C. D., Norbeck A. D., Zhu J. K. et al. 2009 Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell33, 192-203.
44. Reinders J., Wulff B. B., Mirouze M., Mari-Ordonez A., Dapp M., Rozhon W. et al. 2009 Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev. 23, 939-950.
45. Saghai-Maroof M. A., Soliman K. M., Jorgesen R. A. and Allard R. W. 1984 Ribosomal DNA spacer-length polymorphisms in barly Mendelian inheritance, chromosomal location and population dynamics. Proc. Natl. Acad. Sci. USA81, 8014- 8018.
46. Sasaki T., Kobayashi A., Saze H. and Kakutani T. 2012 RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1. Plant J. 70, 750-758.
47. Satheeshkumar P. K. and Gupta A. K. 2012 Cloning of Casuarina equisetifolia chloroplast ribosomal RNA (rRNA) genes and its application in phylogenetic studies. Res. Plant Biol. 2, 30-37.
48. Saze H., Tsugane K., Kanno T. and Nishimura T. 2012 DNA methylation in plants: relationship to small RNAs and histone modifications and functions in transposon inactivation. Plant Cell Physiol. 53, 766-784.
49. Sharma V., Chaudhary S., Srivastava S., Pandey R. and Kumar S. 2012 Characterization of variation and quantitative trait loci related to terpenoid indole alkaloid yield in a recombinant inbred line mapping population of Catharanthus roseus. J. Genet. 91, 49-69.
50. Slaughter A., Daniel X., Flors V., Luna E., Hohn B. and Mauch-Mani B. 2012 Descendants of primed Arabidopsis plants exhibit resistance to biotic stress. Plant Physiol. 158, 835-843.
51. Small R. L., Cronn R. C. and Wendel J. F. 2004 Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 17, 145-170.
52. Song Y., Ji D., Li S., Wang P., Li Q. and Xiang F. 2012 The dynamic changes of DNA methylation and histone modifications of salt responsive transcription factor genes in soybean. PLoS One7, e41274.
53. Teixeira F. K., Heredia F., Sarazin A., Roudier F., Boccara M., Ciaudo C. et al. 2009 A role for RNAi in the selective correction of DNA methylation defects. Science323, 1600-1604.
54. Vaillant I., Tutois S., Jasencakova Z., Douet J., Schubert I. and Tourmente S. 2008 Hypomethylation and hypermethylation of the tandem repetitive 5S rRNA genes in Arabidopsis. Plant J. 54, 299-309.
55. Walsh C. P. and Xu G. L. 2006 Cytosine methylation and DNA repair. Curr. Top. Microbiol. Immunol. 301, 283-315.
56. Wada Y., Miyamoto K., Kusano H. and Sano H. 2004 Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol. Genet. Genomics271, 658-666.
57. Wicke S., Schneeweiss G. M., dePamphilis C. W., Muller K. F. and Quandt D. 2011 The evolution of the plastid chromosome in land plants: gene content, gene order and gene function. Plant Mol. Biol. 76, 273-297.
58. Yang A. S., EsteÂcio M. R. H., Doshi K., Kondo Y., Tajara E. H. and Issa J. J. 2004 A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res. 32, e38.
59. Zhang X., Mathews C. K. 1994 Effect of DNA cytosine methylation upon deamination-induced mutagenesis in a natural target sequence in duplex DNA. J. Biol. Chem. 269, 7066-7069.
60. Zhu J. K. 2009 Active DNA methylation mediated by DNA glycosylases. Ann. Rev. Genet. 43, 143-166.