Editorial epigenetic effects implying repeated sequences and TEs are knowledge about how genotype leads to phenotype, known to occur. We must therefore be aware that the the reviews published in this special issue clearly show environment during one developmental stage can have a that we have already entered the epigenetic area. We subsequent stages and even in adulthood. think that it is in the fields presented above, and by Further studies are therefore required to help decipher the means of a comparative approach involving both m nechanisms involved. Such studies will be confronted and nonmodel species, that the most stimulating the high level of epigenomic variation observed between discoveries will be made in the future. individuals within populations and between different gions, as reported in the review by John Conflict of interest nd Tricker, which outlines the great potential and possible pitfalls of population epigenomics ohannes et al., 2008; The author declares no conflict of interest Vieira et al., 2009), which can be expected to provide a plentiful supply of data that will be difficult to analyze. The Acknowledgements species could bias the analysis and propose that epigenetic I would like to thank Vincent Colot (Institut de biologie, may be more representative of biological normality. the choice of contributing authors This special issue ends with two examples of the alation of tissue development. Covic C Biemont Karaca and Lie summarize recent evidence that behavior Laboratoire de biometrie et Biologie Evolutive, UMR 5558, and environment influence neurogenesis in the adult CNRS, Universite de lyon, Universite Lyon 1 hippocampus through epigenetic mechanisms. It has Villeurbanne france indeed been shown that new neurons are generated in E-mail: biemont@biomserv.univ-lyonl fr the hippocampus throughout life, and because this tissue is associated with learning, memory and emotional References control, any effect of the environment is therefore of great importance for our understanding of human Bayer M, Nawy T, Giglione C, Galli M, Meinnel T, Lukowitz w behavior. The authors highlight the dynamic role (2009). Paternal control of embryonic patterning in Arabidop- DNA methylation and histone methylation through the Polycomb and Trithorax complexes. Cvekl and Mitton Feng S, Cokus s), Zhang x, Chen PY, Bostick M, goll mG et al summarize the roles of sequence-specific DNA-binding (2010). Conservation and divergence of methylation patterning atl Acad sci usA 107: 8689-8t transcription factors in the recruitment to specific Johannes E, Colot V, Jansen rC (2008). Epigenome dy chromosomal regions of chromatin remodeling enzymes quantitative genetics perspective. Nature Rev genet 9: 883-890 and their impact on extracellular signaling and cellular Johannes E, Porcher E, Teixeira FK, Saliba-Colombani V,Simon differentiation during vertebrate eye development and M, Agier n et al.(2009). Assessing the impact of transgene associated diseases. The authors show how changes in omplex traits. PLos Genetics 5 he nucleolar organization, in th e expression noncod- e1000530 ing RNAs and in DNA methylation all contribute to Kacem S, Feil R(2009). Chromatin mechanisms in regulating the development of the lens and retina. The printing Mamm Genome 20: 544-556 epigenetic regulatory mechanisms involved in neurogen- Kristensen TN, Pedersen KS, Vermeulen C], Loeschcke esis and ocular tissues are good illustrations of an Research on inbreeding in the omic era. Trends Ecol exciting new field of research, which should help us to 44-52 decipher the relationships between the environment and Law A, Jacobsen SE(2010). Establishing, maintaining and g dNa methylation patterns in plants and animals development of normal tissue through epigenetic me- Nature Reo Genet 11: 204-220 chanisms and also to understand diseases related to Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti- aging and to changes in the environment in terms of Filippini j et aL. (2009). Human DNA methylome at bas enome size and composition and population structure resolution show widespread epigenomic differences. Nature The last review in this issue deals with the search for 462:315-322. Mathieu o, Reinders J, Caikovski M, Smathajitt C, Paszkowski J with the aim of finding new therapeutic approaches (2007). Transgenerational stability of the arabid and using epigenetic patterns, as prognostic and peaston A, Evsikov av Graber jh, de vries wn, holbrook ae Buysschaert and Lambrechts promote pharmacoepige- Solter D et al.(2004). Retrotransposons regulate host genes in nomics, pointing out that DNA methyltransferases and 597-606. histone deacetylase inhibitors are beginning to be Schilling E, El Chartouni C, Rehli M(2009). Allele-specific DNA accepted as potential candidates for cancer treatment methylation in mouse strains is mainly determined by These agents may reactivate silenced tumor suppressor cis-acting sequences. Genome Res 19: 2028-2035. and apoptotic genes, as well as influencing the tumor Vieira C, Fablet M, Lerat E,(2009). Infra- and transspecific clues Although classical genetic techniques and the high- Zhai Liu Liu B, Li P, Meyers BC, Chen Xet al.(2008).Small includ put sequencing of genomes of various species through ng invertebrates, in which DNA methylation RNA-directed epigenetic natural variation in Arabidopsis issue) will continue to furnish new and important human autosomes. Genome Biol 10: R138epigenetic effects implying repeated sequences and TEs are known to occur. We must therefore be aware that the environment during one developmental stage can have a strong impact on subsequent stages and even in adulthood. Further studies are therefore required to help decipher the mechanisms involved. Such studies will be confronted by the high level of epigenomic variation observed between individuals within populations and between different genomic regions, as reported in the review by Johnson and Tricker, which outlines the great potential and possible pitfalls of population epigenomics (Johannes et al., 2008; Vieira et al., 2009), which can be expected to provide a plentiful supply of data that will be difficult to analyze. The authors then argue that the conventional use of model species could bias the analysis and propose that epigenetic analyses should be extended to nonmodel systems, which may be more representative of biological normality. This special issue ends with two examples of the epigenetic regulation of tissue development. Covic, Karaca and Lie summarize recent evidence that behavior and environment influence neurogenesis in the adult hippocampus through epigenetic mechanisms. It has indeed been shown that new neurons are generated in the hippocampus throughout life, and because this tissue is associated with learning, memory and emotional control, any effect of the environment is therefore of great importance for our understanding of human behavior. The authors highlight the dynamic role of DNA methylation and histone methylation through the Polycomb and Trithorax complexes. Cvekl and Mitton summarize the roles of sequence-specific DNA-binding transcription factors in the recruitment to specific chromosomal regions of chromatin remodeling enzymes, and their impact on extracellular signaling and cellular differentiation during vertebrate eye development and associated diseases. The authors show how changes in the nucleolar organization, in the expression of noncod￾ing RNAs and in DNA methylation all contribute to regulating the development of the lens and retina. The epigenetic regulatory mechanisms involved in neurogen￾esis and ocular tissues are good illustrations of an exciting new field of research, which should help us to decipher the relationships between the environment and development of normal tissue through epigenetic me￾chanisms and also to understand diseases related to aging and to changes in the environment in terms of genome size and composition and population structure. The last review in this issue deals with the search for the epigenetic processes that underpin tumor biology, with the aim of finding new therapeutic approaches and using epigenetic patterns as prognostic and predictive biomarkers in cancer therapy. Finally, Claes, Buysschaert and Lambrechts promote pharmacoepige￾nomics, pointing out that DNA methyltransferases and histone deacetylase inhibitors are beginning to be accepted as potential candidates for cancer treatment. These agents may reactivate silenced tumor suppressor and apoptotic genes, as well as influencing the tumor environment. Although classical genetic techniques and the high￾throughput sequencing of genomes of various species (including invertebrates, in which DNA methylation seems to have functions different from those it has in plants and vertebrates, and which are not covered in this issue) will continue to furnish new and important knowledge about how genotype leads to phenotype, the reviews published in this special issue clearly show that we have already entered the epigenetic area. We think that it is in the fields presented above, and by means of a comparative approach involving both model and nonmodel species, that the most stimulating discoveries will be made in the future. Conflict of interest The author declares no conflict of interest. Acknowledgements I would like to thank Vincent Colot (Institut de Biologie, Ecole Normale Supe´rieure, Paris, France) for his help in the choice of contributing authors. C Bie´mont Laboratoire de Biome´trie et Biologie Evolutive, UMR 5558, CNRS, Universite´ de Lyon, Universite´ Lyon 1, Villeurbanne, France E-mail: biemont@biomserv.univ-lyon1.fr References Bayer M, Nawy T, Giglione C, Galli M, Meinnel T, Lukowitz W (2009). Paternal control of embryonic patterning in Arabidop￾sis thaliana. Science 323: 1485–1488. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG et al. (2010). Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107: 8689–8694. Johannes F, Colot V, Jansen RC (2008). Epigenome dynamics: a quantitative genetics perspective. Nature Rev Genet 9: 883–890. Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N et al. (2009). Assessing the impact of transgenera￾tional epigenetic variation on complex traits. PLoS Genetics 5: e1000530. Kacem S, Feil R (2009). Chromatin mechanisms in genomic imprinting. Mamm Genome 20: 544–556. Kristensen TN, Pedersen KS, Vermeulen CJ, Loeschcke V (2009). Research on inbreeding in the ‘omic’ era. Trends Ecol Evol 25: 44–52. Law JA, Jacobsen SE (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Rev Genet 11: 204–220. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti￾Filippini J et al. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315–322. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J (2007). Transgenerational stability of the Arabidopsis epi￾genome is coordinated by CG methylation. Cell 130: 851–862. Peaston A, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D et al. (2004). Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7: 597–606. Schilling E, El Chartouni C, Rehli M (2009). Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences. Genome Res 19: 2028–2035. Vieira C, Fablet M, Lerat E (2009). Infra- and transspecific clues to understanding the dynamics of transposable elements. Genome Dyn Stab (doi:10.1007/7050_2009_1044). Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X et al. (2008). Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet 4: e1000056. Zhang Y, Rohde C, Reinhardt R, Voelcker-Rehage C, Jeltsch A (2009). Non-imprinted allele-specific DNA methylation on human autosomes. Genome Biol 10: R138. Editorial 3 Heredity