EpiRADseq: Scalable analysis of genomewide patterns of methylation using next-generation sequencing

Methods in Ecology and Evolution

Volumn 7, Issue 1, 2016, Pages 60-69

  Schield, Drew R ^a   Walsh, Matthew R ^a   Card, Daren C ^a   Andrew, Audra L ^a   Adams, Richard H ^a   Castoe, Todd A ^a  

^a UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

Author keywords

CpG methylation; Daphnia; Epigenetics; High throughput methylation measurement; Restriction site associated DNA sequencing; Transgenerational shift

Indexed keywords

EID: 84939226446     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12435     Document Type: Article

References (47)

1. Arnold, B., Corbett-Detig, R.B., Hartl, D. & Bomblies, K. (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, 22, 3179-3190.
2. Balthazart, J. & Ball, G.F. (1995) Sexual differentiation of brain and behavior in birds. Trends in Endocrinology & Metabolism, 6, 21-29.
3. Bell, J.T., Tsai, P.C., Yang, T.P., Pidsley, R., Nisbet, J., Glass, D. et al. (2012) Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genetics, 8, 189-200.
4. Bird, A.P. (1985) CpG-rich islands and the function of DNA methylation. Nature, 321, 209-213.
5. Bird, A.P., Taggart, M.H. & Smith, B.A. (1979) Methylated and unmethylated DNA compartments in the sea urchin genome. Cell, 17, 889-901.
6. Bolger, A.M., Lohse, M. & Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114-2120.
7. Catchen, J., Hohenlohe, P.A., Bassham, S., Amores, A. & Cresko, W.A. (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140.
8. Chong, Z., Ruan, J. & Wu, C.I. (2012) Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads. Bioinformatics, 28, 2732-2737.
9. Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H. et al. (2011) The ecoresponsive genome of Daphnia pulex. Science, 331, 555-561.
10. Cox, R.M., Stenquist, D.S. & Calsbeek, R. (2009) Testosterone, growth and the evolution of sexual size dimorphism. Journal of Evolutionary Biology, 22, 1586-1598.
11. Denver, R.J. (1997) Proximate mechanisms of phenotypic plasticity in amphibian metamorphosis. American Zoologist, 37, 172-184.
12. Hammoud, S.S., Nix, D.A., Hammoud, A.O., Gibson, M., Cairns, B.R. & Carrell, D.T. (2011) Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men. Human Reproduction, 26, 2558-2569.
13. Herrera, C.M. & Bazaga, P. (2010) Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytologist, 187, 867-876.
14. Hutchins, E.D., Markov, G.J., Eckalbar, W.L., George, R.M., King, J.M., Tokuyama, M.A. et al. (2014) Transcriptomic analysis of tail regeneration in the lizard Anolis carolinensis reveals activation of conserved vertebrate developmental and repair mechanisms. PLoS ONE, 9, e105004.
15. Jablonka, E. & Raz, G. (2009) Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Quarterly Review of Biology, 84, 131-176.
16. Jaenisch, R. & Bird, A. (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genetics, 33, 245-254.
17. Kilvitis, H.J., Alvarez, M., Foust, C.M., Schrey, A.W., Robertson, M. & Richards, C.L. (2014) Ecological epigenetics. Ecological Genomics: Ecology and the Evolution of Genes and Genomes, 781, 191-210.
18. Konstantinides, N. & Averof, M. (2014) A common cellular basis for muscle regeneration in arthropods and vertebrates. Science, 343, 788-791.
19. Kronforst, M.R., Gilley, D.C., Strassmann, J.E. & Queller, D.C. (2008) DNA methylation is widespread across social Hymenoptera. Current Biology, 18, R287-R288.
20. Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
21. Li, W.Z. & Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
22. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. & Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
23. Martienssen, R.A. & Colot, V. (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science, 293, 1070-1074.
24. Massicotte, R., Whitelaw, E. & Angers, B. (2011) DNA methylation: a source of random variation in natural populations. Epigenetics, 6, 422-428.
25. Miner, B.E., De Meester, L., Pfrender, M.E., Lampert, W. & Hairston, N.G. Jr (2012) Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. Proceedings of the Royal Society B: Biological Sciences, 279, 1873-1882.
26. Monaghan, J.R., Walker, J.A., Page, R.B., Putta, S., Beachy, C.K. & Voss, S.R. (2007) Early gene expression during natural spinal cord regeneration in the salamander Ambystoma mexicanum. Journal of Neurochemistry, 101, 27-40.
27. Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S. & Hoekstra, H.E. (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7, e37135.
28. Post, D.M., Palkovacs, E.P., Schielke, E.G. & Dodson, S.I. (2008) Intraspecific variation in a predator affects community structure and cascading trophic interactions. Ecology, 89, 2019-2032.
29. Regev, A., Lamb, M.J. & Jablonka, E. (1998) The role of DNA methylation in invertebrates: developmental regulation or genome defense? Molecular Biology & Evolution, 15, 880-891.
30. Reyna-Lopez, G.E., Simpson, J. & Ruiz-Herrera, J. (1997) Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Molecular & General Genetics, 253, 703-710.
31. Richards, C.L., Boruta, M., Bossdorf, O., Coon, C.A.C., Foust, C.M., Hughes, A.R. et al. (2013) Epigenetic mechanisms of phenotypic plasticity. Integrative and Comparative Biology, 53, E179-E179.
32. Riessen, H.P. (1999) Predator-induced life history shifts in Daphnia: a synthesis of studies using meta-analysis. Canadian Journal of Fisheries & Aquatic Sciences, 56, 2487-2494.
33. Robinson, M.D., McCarthy, D.J. & Smyth, G.K. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
34. Saviola, A.J., Pla, D., Sanz, L., Castoe, T.A., Calvete, J.J. & Mackessy, S.P. (2015) Comparative venomics of the Prairie Rattlesnake (Crotalus viridis viridis) from Colorado: identification of a novel pattern of ontogenetic changes in venom composition and assessment of the immunoreactivity of the commercial antivenom CroFab(R). Journal of Proteomics, 121, 28-43.
35. Schield, D.R., Walsh, M.R., Card, D.C., Andrew, A.L., Adams, R.H. & Castoe, T.A. (2015) Data from: EpiRADseq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing. Dryad Data Repository, http://dx.doi.org/10.5061/dryad.hs200.
36. Schrey, A., Alvarez, M., Foust, C., Kilvitis, H., Liebl, A., Martin, L.B., Richards, C. & Robertson, M. (2013) Ecological epigenetics: beyond MS-AFLP. Integrative and Comparative Biology, 53, E191-E191.
37. Shinoda, T. & Itoyama, K. (2003) Juvenile hormone acid methyltransferase: a key regulatory enzyme for insect metamorphosis. Proceedings of the National Academy of Sciences USA, 100, 11986-11991.
38. Stibor, H. (1992) Predator induced life history shifts in a freshwater cladoceran. Oecologia, 92, 162-165.
39. Stollewerk, A. (2010) The water flea Daphnia - a 'new' model system for ecology and evolution? Journal of Biology, 9, 21.
40. Suzuki, M.M. & Bird, A. (2008) DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics, 9, 465-476.
41. Tweedie, S., Charlton, J., Clark, V. & Bird, A. (1997) Methylation of genomes and genes at the invertebrate-vertebrate boundary. Molecular and Cellular Biology, 17, 1469-1475.
42. Vandegehuchte, M.B., Lemiere, F., Vanhaecke, L., Vanden Berghe, W. & Janssen, C.R. (2010) Direct and transgenerational impact on Daphnia magna of chemicals with a known effect on DNA methylation. Comparative Biochemistry and Physiology C-Toxicology & Pharmacology, 151, 278-285.
43. Walsh, M.R. & Post, D.M. (2011) Interpopulation variation in a fish predator drives evolutionary divergence in prey in lakes. Proceedings of the Royal Society B: Biological Sciences, 278, 2628-2637.
44. Walsh, M.R. & Post, D.M. (2012) The impact of intraspecific variation in a fish predator on the evolution of phenotypic plasticity and investment in sex in Daphnia ambigua. Journal of Evolutionary Biology, 25, 80-89.
45. Walsh, M.R., Cooley, F., Biles, K. & Munch, S.B. (2015) Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory? Proceedings of the Royal Society B: Biological Sciences, 282, 20142205.
46. Yaish, M.W., Colasanti, J. & Rothstein, S.J. (2011) The role of epigenetic processes in controlling flowering time in plants exposed to stress. Journal of Experimental Botany, 62, 3727-3735.
47. Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T. & Henikoff, S. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics, 39, 61-69.