Natural Epigenetic variation in the female great roundleaf bat (Hipposideros armiger) populations

Molecular Genetics and Genomics

Volumn 287, Issue 8, 2012, Pages 643-650

  Liu, Sen ^a,b   Sun, Keping ^a   Jiang, Tinglei ^a   Ho, Jennifer P ^b   Liu, Bao ^a   Feng, Jiang ^a  

^a NORTHEAST NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Chiroptera; DNA methylation; Mammal; MSAP

Indexed keywords

BAT; DNA METHYLATION; EPIGENETICS; FEMALE; GENE AMPLIFICATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GREAT ROUNDLEAF BAT; METHYLATION SENSITIVE AMPLIFIED POLYMORPHISM; NONHUMAN; PRIORITY JOURNAL; REVIEW;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; CHIROPTERA; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; FEMALE; GENETIC VARIATION;

ANIMALIA; CHIROPTERA; HIPPOSIDEROS ARMIGER; MAMMALIA;

EID: 84864710693     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-012-0704-x     Document Type: Review

References (59)

1. Agrawal AA (2001) Phenotypic plasticity in the interactions and evolution of species. Science 294:321-326. doi:10.1126/science. 1060701
2. Allis CD, Jenuwein T, Reinberg D, Caparros ML (2007) Epigenetics. CSHL Press, New York
3. Angers B, Castonguay E, Massicotte R (2010) Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Mol Ecol 19:1283-1295. doi:10.1111/j.1365-294X. 2010.04580.x
4. Ashikawa I (2001) Surveying CpG methylation at 50-CCGG in the genomes of rice cultivars. Plant Mol Biol 45:31-39. doi:10. 1023/A:1006457321781
5. Bassam BJ, Caetano-Anollés G, Gresshoff P (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80-83. doi:10.1016/0003-2697 (91) 90120-I
6. Bird A (2007) Perceptions of epigenetics. Nature 447:396-398. doi: 10.1038/nature05913
7. Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, Cui H, Yu W, Rongione MA, Ekström TJ, Harris TB (2008) Intra-individual change in DNA methylation over time with familial clustering. J Am Med Assoc 299:2877-2883. doi:10. 1001/jama.299.24.2877
8. Blouin MS, Thuillier V, Cooper B, Amarasinghe V, Cluzel L, Araki H, Grunau C (2010) No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss). Can J Fish Aquat Sci 67:217-224. doi: 10.1139/F09-174
9. Bonasio R, Tu S, Reinberg D (2010) Molecular signals of epigenetic states. Science 330:612-616. doi:10.1126/science.1191078
10. Bossdorf O, Richards CL, Pigliucci M (2008) Epigenetics for ecologists. Ecol Lett 11:106-115. doi:10.1111/j.1461-0248.2007.01130.x
11. Bossdorf O, Arcuri D, Richards CL, Pigliucci M (2010) Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana. Evol Ecol 24:541-553. doi:10.1007/s10682-010-9372-7
12. Bussell JD (1999) The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae). Mol Ecol 8:775-789. doi:10.1046/j.1365-294X. 1999.00627.x
13. Caballero A, Quesada H, Rolan-Alvarez E (2008) Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 179:539-554. doi:10.1534/genetics.107.083246
14. Cervera MT, Ruiz-García L, Martínez-Zapater J (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylationsensitive AFLP markers. Mol Genet Genomics 268:543-552. doi:10.1007/s00438-002-0772-4
15. Dolédec S, Chessel D (1994) Co-inertia analysis: an alternative method for studying species-environment relationships. Freshw Biol 31:277-294. doi:10.1111/j.1365-2427.1994.tb01741.x
16. Dolinoy DC, Huang D, Jirtle RL (2007) Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. Proc Natl Acad Sci USA 104:13056-13061. doi:10.1073/pnas.0703739104
17. Ehrlich M, Wang RY (1981) 5-Methylcytosine in eukaryotic DNA. Science 212:1350-1357. doi:10.1126/science.6262918
18. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, Gehrke C (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells. Nucleic Acids Res 10:2709-2721. doi:10.1093/nar/10. 8.2709
19. Gao L, Geng Y, Li BO, Chen J, Yang JI (2010) Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation. Plant Cell Environ 33:1820-1827. doi:10.1111/j.1365-3040.2010.02186.x
20. Herrera CM, Bazaga P (2010) Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytol 187:867-876. doi:10.1111/j.1469-8137.2010.03298.x
21. Herrera CM, Bazaga P (2011) Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long term inequality in herbivory. Mol Ecol 20:1675-1688. doi:10.1111/j.1365-294X.2011. 05026.x
22. Jablonka E, Raz G (2009) Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Q Rev Biol 84:131-176. doi:10.1086/598822
23. Jablonka E, Lamb MJ, Zeligowski A (2005) Evolution in four dimensions. The MIT Press, London
24. Jablonski D (2004) Extinction: past and present. Nature 427:589. doi: 10.1038/427589a
25. Jones G, Jacobs DS, Kunz TH, Willig MR, Racey PA (2009) Carpe noctem: the importance of bats as bioindicators. Endanger Species Res 8:93-115. doi:10.3354/esr00182
26. Keyte AL, Percifield R, Liu B, Wendel JF (2006) Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). J Hered 97:444-450. doi:10.1093/jhered/esl023
27. Kucharski R, Maleszka J, Foret S, Maleszka R (2008) Nutritional control of reproductive status in honeybees via DNA methylation. Science 319:1827-1830. doi:10.1126/science.1153069
28. Li Y, Shan X, Liu X, Hu L, Guo W, Liu B (2008) Utility of the methylation-sensitive amplified polymorphism (MSAP) marker for detection of DNA methylation polymorphism and epigenetic population structure in a wild barley species (Hordeum brevisubulatum). Ecol Res 23:927-930. doi:10.1007/s11284-007- 0459-8
29. Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Meyer P (2010) Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One 5:e10326. doi:10.1371/journal.pone.0010326
30. Liu J, Hutchison K, Perrone-Bizzozero N, Morgan M, Sui J, Calhoun V (2010) Identification of genetic and epigenetic marks involved in population structure. PLoS One 5:e13209. doi:10.1371/journal.pone.0013209
31. Mann MB, Smith HO (1977) Specificity of Hpa II and Hae II DNA methylases. Nucleic Acids Res 4:4211-4222. doi:10.1093/nar/4.12.4211
32. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220
33. Massicotte R, Whitelaw E, Angers B (2011) DNA methylation: a source of random variation in natural populations. Epigenetics 6:421-427. doi:10.4161/epi.6.4.14532
34. McClelland M, Nelson M, Raschke E (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 22:3640-3659. doi: 10.1093/nar/22.17.3640
35. Meaney MJ, Ferguson-Smith AC (2010) Epigenetic regulation of the neural transcriptome: the meaning of the marks. Nat Neurosci 13:1313-1318. doi:10.1038/nn1110-1313
36. Michaud EJ, Van Vugt M, Bultman SJ, Sweet HO, Davisson MT, Woychik RP (1994) Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. Genes Dev 8:1463-1472. doi: 10.1101/gad.8.12.1463
37. Migicovsky Z, Kovalchuk I (2011) Frontiers: epigenetic memory in mammals. Front Epigenomics. doi:10.3389/fgene.2011.00028
38. Morán P, Pérez-Figueroa A (2011) Methylation changes associated with early maturation stages in the Atlantic salmon. BMC Genet 12:86. doi:10.1186/1471-2156-12-86
39. Morgan HD, Sutherland HGE, Martin DIK, Whitelaw E (1999) Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 23:314-318. doi:10.1038/15490
40. Norberg UM, Rayner JMV (1987) Ecological morphology and flight in bats (Mammalia; Chiroptera): wing adaptations, flight performance, foraging strategy and echolocation. Philos Trans R Soc B 316:335-427. doi:10.1098/rstb.1987.0030
41. Ochogavía AC, Cervigni G, Selva JP, Echenique VC, Pessino SC (2009) Variation in cytosine methylation patterns during ploidy level conversions in Eragrostis curvula. Plant Mol Biol 70:17-29. doi:10.1007/s11103- 009-9454-5
42. Parisod C, Christin PA (2008) Genome wide association to fine scale ecological heterogeneity within a continuous population of Biscutella laevigata (Brassicaceae). New Phytol 178:436-447. doi:10.1111/j.1469-8137.2007.02361.x
43. Parisod C, Trippi C, Galland N (2005) Genetic variability and founder effect in the pitcher plant Sarracenia purpurea (Sarraceniaceae) in populations introduced into Switzerland: from inbreeding to invasion. Ann Bot Lond 95:277-286. doi:10.1093/aob/mci023
44. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223-225. doi:10.2307/2409177
45. Richards EJ (2006) Inherited epigenetic variation-revisiting soft inheritance. Nat Rev Genet 7:395-401. doi:10.1038/nrg1834
46. Richards EJ (2008) Population epigenetics. Curr Opin Genet Dev 18:221-226. doi:10.1016/j.gde.2008.01.014
47. Richards CL, Bossdorf O, Verhoeven KJF (2010) Understanding natural epigenetic variation. New Phytol 187:562-564. doi:10. 1111/j.1469-8137.2010. 03369.x
48. Rosenberg MS, Anderson CD (2011) PASSaGE: pattern analysis, spatial statistics and geographic exegesis. Version 2. Method Ecol Evol 2:229-232. doi:10.1111/j.2041-210X.2010.00081.x
49. Schrey AW, Coon CAC, Grispo MT, Awad M, Imboma T, McCoy ED, Mushinsky HR, Richards CL, Martin LB (2012) Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus) on two continents. Genet Res Int. doi:10.1155/2012/979751
50. Skinner MK, Guerrero-Bosagna C (2009) Environmental signals and transgenerational epigenetics. Epigenomics 1:111-117. doi:10. 2217/EPI.09.11
51. Sneath PHA, Sokal RR (1973) Numerical taxonomy. The principles and practice of numerical classification. WH Freeman, San Francisco
52. Thioulouse J, Chessel D, Dolédec S, Olivier JM (1997) ADE-4: a multivariate analysis and graphical display software. Stat Comput 7:75-83. doi:10.1023/A:1018513530268
53. Vaughn MW, Tanurdži M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 5:e174. doi:10.1371/journal.pbio.0050174
54. Vogt G, Huber M, Thiemann M, Van Den Boogaart G, Schmitz OJ, Schubart CD (2008) Production of different phenotypes from the same genotype in the same environment by developmental variation. J Exp Biol 211:510-523. doi:10.1242/jeb.008755
55. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414. doi: 10.1093/nar/23.21.4407
56. Waalwijk C, Flavell RA (1978) Msp I, an isoschizomer of Hpa II which cleaves both unmethylated and methylated Hpa II sites. Nucleic Acids Res 5:3231-3236. doi:10.1093/nar/5.9.3231
57. Xu M, Li XQ, Korban S (2000) AFLP-based detection of DNA methylation. Plant Mol Biol Rep 18:361-368. doi:10.1007/BF 02825064
58. Zhang RZ, Jin SK, Quan GQ, Li SH, Ye Z, Wang FG, Zhang ML (1997) Distribution of mammalian species in China. China Forestry Publishing House, Beijing
59. Zhang D, Cheng L, Badner JA, Chen C, Chen Q, Luo W, Craig DW, Redman M, Gershon ES, Liu C (2010) Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet 86:411-419. doi:10.1016/j.ajhg.2010. 02.005