Table II.10. Life history events that alter the epigenome (DNA methylation and chromatin formatting).

Event (Organism)



Polyploidy (plants)

Histone acetylation changes

 (Chen and Tian 2007)

Allopolyploidy (plants)

Changes in methylation patterns of mobile elements

 (Dong, Liu et al. 2005)

Synthetic allotetraploids

Remodeling of DNA methylation, phenotypic and transcriptional changes


 (Madlung, Masuelli et al. 2002; Ha, Lu et al. 2009)

Interspecific hybrids (plants)

Altered DNA methylation patterns; Phenotypic and epigenetic variability

 (Salmon, Ainouche et al. 2005; Marfil, Camadro et al. 2009)

Introgression from Zizania latifolia into rice

Extensive alterations in DNA methylation

 (Liu, Wang et al. 2004)

Incompatible cross-pollination (rice)

Transgenerational epigenetic instability.

 (Wang, Chai et al. 2009)

Tissue culture growth

Altered mPing transposon cytosine methylation

(Ngezahayo, Xu et al. 2009)

Tobacco tissue culture

Gradual and frequent epigenetic reprogramming of invertedly repeated transgene epialleles

(Krizova, Fojtova et al. 2009)

Immortalized Arabidopsis cell suspension culture

Euchromatin DNA hypermethylation and DNA hypomethylation of specific transposable elements

(Tanurdzic, Vaughn et al. 2008)

Antibiotics and tissue culture (tobacco)

Genome-wide hypermethylation

 (Schmitt, Oakeley et al. 1997)

Rice plants subjected to space flight

Heritable hypermethylation of TEs and other sequences

 (Ou, Long et al. 2009)

Interspecific hybrids (mouse)

Placental DNA methylation changes

 (Schutt, Florl et al. 2003)

Interspecific hybrid (mouse)

Methylation perturbations in retroelements

 (Brown, Golden et al. 2008)

Interspecific hybrids (Peromyscus mice)

Genomic imprinting disrupted

 (Vrana, Guan et al. 1998)

Interspecific hybrids (Wallabies)

Loss of retroelement methylation

(O'Neill, O'Neill et al. 1998)

X irradiation

Transgenerational cancers and modifications in DNA methylation

 (Koturbash, Baker et al. 2006)

Particulate air pollution (Mouse)

DNA global hypermethylation

 (Yauk, Polyzos et al. 2008)

Nutrition (mouse)

Retrotransposon methylation in response to dietary methionine

 (Waterland and Jirtle 2003)

Wolbachia endosymbiosis in Drosophila males

Sperm chromatin remodeling; cytoplasmic incompatibility

 (Harris and Braig 2003)

Wolbachia endosymbiosis in leafhopper (Zyginidia pullula) males

Feminization, sterility, female-specific DNA methylation patterns

 (Negri, Franchini et al. 2009)

Bacterial infection (human)

Histone modifications and chromatin remodeling (particularly immune cells)

 (Arbibe 2008; Hamon and Cossart 2008)

Bacterial infection (mice)

DNA hypermethylation

(Bobetsis, Barros et al. 2007)

Fungal infection (tobacco)

Transgenerational instability

 (Boyko, Kathiria et al. 2007)

Helicobacter infection (human)

LINE-1 hypomethylation

 (Yamamoto, Toyota et al. 2008)

Helicobacter infection (human)

Aberrant or hypermethylation of CpG islands

 (Maekita, Nakazawa et al. 2006; Nardone, Compare et al. 2007; Nardone and Compare 2008; Moriichi, Watari et al. 2009; Nakajima, Yamashita et al. 2009; Hong, Oh et al. 2010; Yoshida, Yamashita et al. 2011)

Campylobacter rectus infection of the placenta (human)

DNA methylation and histone modification changes

(Minarovits 2009)




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Bobetsis, Y. A., S. P. Barros, et al. (2007). "Bacterial infection promotes DNA hypermethylation." J Dent Res 86(2): 169-174.

Boyko, A., P. Kathiria, et al. (2007). "Transgenerational changes in the genome stability and methylation in pathogen-infected plants: (virus-induced plant genome instability)." Nucleic Acids Res 35(5): 1714-1725.

Brown, J. D., D. Golden, et al. (2008). "Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation." Genomics 91(3): 267-273.

Chen, Z. J. and L. Tian (2007). "Roles of dynamic and reversible histone acetylation in plant development and polyploidy." Biochim Biophys Acta 1769(5-6): 295-307.

Dong, Y. Z., Z. L. Liu, et al. (2005). "Allopolyploidy in wheat induces rapid and heritable alterations in DNA methylation patterns of cellular genes and mobile elements." Genetika 41(8): 1089-1095.

Ha, M., J. Lu, et al. (2009). "Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids." Proc Natl Acad Sci U S A 106(42): 17835-17840.

Hamon, M. A. and P. Cossart (2008). "Histone modifications and chromatin remodeling during bacterial infections." Cell Host Microbe 4(2): 100-109.

Harris, H. L. and H. R. Braig (2003). "Sperm chromatin remodelling and Wolbachia-induced cytoplasmic incompatibility in Drosophila." Biochem Cell Biol 81(3): 229-240.

Hong, S. J., J. H. Oh, et al. (2010). "The overmethylated genes in Helicobacter pylori-infected gastric mucosa are demethylated in gastric cancers." BMC Gastroenterol 10: 137.

Koturbash, I., M. Baker, et al. (2006). "Epigenetic dysregulation underlies radiation-induced transgenerational genome instability in vivo." Int J Radiat Oncol Biol Phys 66(2): 327-330.

Krizova, K., M. Fojtova, et al. (2009). "Cell culture-induced gradual and frequent epigenetic reprogramming of invertedly repeated tobacco transgene epialleles." Plant Physiol 149(3): 1493-1504.

Liu, Z., Y. Wang, et al. (2004). "Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia." Plant Mol Biol 54(4): 571-582.

Madlung, A., R. W. Masuelli, et al. (2002). "Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids." Plant Physiol 129(2): 733-746.

Maekita, T., K. Nakazawa, et al. (2006). "High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk." Clin Cancer Res 12(3 Pt 1): 989-995.

Marfil, C. F., E. L. Camadro, et al. (2009). "Phenotypic instability and epigenetic variability in a diploid potato of hybrid origin, Solanum ruiz-lealii." BMC Plant Biol 9: 21.

Minarovits, J. (2009). "Microbe-induced epigenetic alterations in host cells: the coming era of patho-epigenetics of microbial infections. A review." Acta Microbiol Immunol Hung 56(1): 1-19.

Moriichi, K., J. Watari, et al. (2009). "Effects of Helicobacter pylori infection on genetic instability, the aberrant CpG island methylation status and the cellular phenotype in Barrett's esophagus in a Japanese population." Int J Cancer 124(6): 1263-1269.

Nakajima, T., S. Yamashita, et al. (2009). "The presence of a methylation fingerprint of Helicobacter pylori infection in human gastric mucosae." Int J Cancer 124(4): 905-910.

Nardone, G. and D. Compare (2008). "Epigenetic alterations due to diet and Helicobacter pylori infection in gastric carcinogenesis." Expert Rev Gastroenterol Hepatol 2(2): 243-248.

Nardone, G., D. Compare, et al. (2007). "Helicobacter pylori and epigenetic mechanisms underlying gastric carcinogenesis." Dig Dis Sci 25(3): 225-229.

Negri, I., A. Franchini, et al. (2009). "Unravelling the Wolbachia evolutionary role: the reprogramming of the host genomic imprinting." Proc Biol Sci 276(1666): 2485-2491.

Ngezahayo, F., C. Xu, et al. (2009). "Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice." BMC Plant Biol 9: 91.

O'Neill, R. J., M. J. O'Neill, et al. (1998). "Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid." Nature 393(6680): 68-72.

Ou, X., L. Long, et al. (2009). "Spaceflight induces both transient and heritable alterations in DNA methylation and gene expression in rice (Oryza sativa L.)." Mutat Res 662(1-2): 44-53.

Salmon, A., M. L. Ainouche, et al. (2005). "Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae)." Mol Ecol 14(4): 1163-1175.

Schmitt, F., E. J. Oakeley, et al. (1997). "Antibiotics induce genome-wide hypermethylation in cultured Nicotiana tabacum plants." J Biol Chem 272(3): 1534-1540.

Schutt, S., A. R. Florl, et al. (2003). "DNA methylation in placentas of interspecies mouse hybrids." Genetics 165(1): 223-228.

Tanurdzic, M., M. W. Vaughn, et al. (2008). "Epigenomic consequences of immortalized plant cell suspension culture." PLoS Biol 6(12): 2880-2895.

Vrana, P. B., X. J. Guan, et al. (1998). "Genomic imprinting is disrupted in interspecific Peromyscus hybrids." Nat Genet 20(4): 362-365.

Wang, H., Y. Chai, et al. (2009). "Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability." BMC Plant Biol 9: 63.

Waterland, R. A. and R. L. Jirtle (2003). "Transposable elements: targets for early nutritional effects on epigenetic gene regulation." Mol Cell Biol 23(15): 5293-5300.

Yamamoto, E., M. Toyota, et al. (2008). "LINE-1 hypomethylation is associated with increased CpG island methylation in Helicobacter pylori-related enlarged-fold gastritis." Cancer Epidemiol Biomarkers Prev 17(10): 2555-2564.

Yauk, C., A. Polyzos, et al. (2008). "Germ-line mutations, DNA damage, and global hypermethylation in mice exposed to particulate air pollution in an urban/industrial location." Proc Natl Acad Sci U S A 105(2): 605-610.

Yoshida, T., S. Yamashita, et al. (2011). "Alu and Satalpha hypomethylation in Helicobacter pylori-infected gastric mucosae." Int J Cancer 128(1): 33-39.