I. Ahmed, A. Sarazin, C. Bowler, V. Colot, and H. Quesneville, Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis, Nucleic Acids Research, vol.39, issue.16, pp.6919-6950, 2011.
DOI : 10.1093/nar/gkr324

M. Arteaga-vazquez and V. Chandler, Paramutation in maize: RNA mediated trans-generational gene silencing, Current Opinion in Genetics & Development, vol.20, issue.2, pp.156-63, 2010.
DOI : 10.1016/j.gde.2010.01.008

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859986

T. Baubec, D. Colombo, C. Wirbelauer, J. Schmidt, and L. Burger, Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation, Nature, vol.17, issue.7546, pp.243-290, 2015.
DOI : 10.1186/gb-2009-10-3-r25

D. Baulcombe and C. Dean, Epigenetic Regulation in Plant Responses to the Environment, Cold Spring Harbor Perspectives in Biology, vol.6, issue.9, p.19471, 2014.
DOI : 10.1101/cshperspect.a019471

C. Becker, J. Hagmann, M. ¨. , J. Koenig, D. Stegle et al., Spontaneous epigenetic variation in the Arabidopsis thaliana methylome, Nature, vol.29, issue.7376, pp.245-294, 2011.
DOI : 10.1038/nature10555

J. Bender, DNA Methylation of the Endogenous PAI Genes in Arabidopsis, Cold Spring Harbor Symposia on Quantitative Biology, vol.153, issue.0, pp.145-53, 2004.
DOI : 10.1126/science.1079695

T. Bestor, V. Chandler, and A. Feinberg, Epigenetic effects in eukaryotic gene expression, Developmental Genetics, vol.5, issue.6, pp.458-6238, 1994.
DOI : 10.1002/dvg.1020150603

A. Bewick, J. L. Niederhuth, C. Willing, E. Hofmeister, and B. , On the origin and evolutionary consequences of gene body DNA methylation, Proceedings of the National Academy of Sciences, vol.113, issue.32, pp.9111-9127, 2016.
DOI : 10.1073/pnas.1604666113

A. Bird, Perceptions of epigenetics, Nature, vol.93, issue.7143, pp.396-98, 2007.
DOI : 10.1038/nature05913

T. Blevins, R. Podicheti, V. Mishra, M. Marasco, and J. Wang, Author response, eLife, vol.299, issue.80, pp.1-22, 2015.
DOI : 10.7554/eLife.09591.039

D. Bond and D. Baulcombe, Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana, PNAS, vol.112, issue.3, p.201413053, 2015.

O. Bossdorf, C. Richards, and M. Pigliucci, Epigenetics for ecologists, Ecology Letters, vol.5, issue.0, pp.106-121, 2008.
DOI : 10.1038/ng1929

B. Brachi, G. Morris, and J. Borevitz, Genome-wide association studies in plants: the missing heritability is in the field, Genome Biology, vol.12, issue.10, p.232, 2011.
DOI : 10.1038/nrg3002

D. Briggs and S. Walters, Plant Variation and Evolution, 1984.
DOI : 10.1017/CBO9781139060196

R. Brink, A genetic change associated with the R locus in maize which is directed and potentially reversible, Genetics, vol.41, issue.6, p.872, 1956.

J. Calarco, F. Borges, M. Donoghue, F. Van-ex, and P. Jullien, Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA, Cell, vol.151, issue.1, pp.194-205, 2012.
DOI : 10.1016/j.cell.2012.09.001

J. Cao, K. Schneeberger, S. Ossowski, G. ¨. , T. Bender et al., Whole-genome sequencing of multiple Arabidopsis thaliana populations, Nature Genetics, vol.155, issue.10, pp.43956-63, 2011.
DOI : 10.1016/j.ajhg.2009.01.005

R. Chodavarapu, S. Feng, B. Ding, S. Simon, and D. Lopez, Transcriptome and methylome interactions in rice hybrids, Proceedings of the National Academy of Sciences, vol.109, issue.30, pp.12040-12085, 2012.
DOI : 10.1073/pnas.1209297109

M. Cleaton, C. Edwards, and A. Ferguson-smith, Phenotypic Outcomes of Imprinted Gene Models in Mice: Elucidation of Pre- and Postnatal Functions of Imprinted Genes, Annual Review of Genomics and Human Genetics, vol.15, issue.1, pp.93-126, 2014.
DOI : 10.1146/annurev-genom-091212-153441

S. Cokus, S. Feng, X. Zhang, Z. Chen, and B. Merriman, Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature, vol.20, issue.7184, pp.215-234, 2008.
DOI : 10.1038/nature06745

D. Coleman-derr and D. Zilberman, Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes, PLoS Genetics, vol.8, issue.10, p.1002988, 2012.
DOI : 10.1371/journal.pgen.1002988.s028

M. Colomé-tatché, S. Cortijo, R. Wardenaar, L. Morgado, and B. Lahouze, Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation, Proceedings of the National Academy of Sciences, vol.109, issue.40, pp.16240-16285, 2012.
DOI : 10.1073/pnas.1212955109

S. Cortijo, R. Wardenaar, M. Colomé-tatché, A. Gilly, and M. Etcheverry, Mapping the Epigenetic Basis of Complex Traits, Science, vol.343, issue.6175, pp.1145-1193, 2014.
DOI : 10.1126/science.1248127

URL : https://hal.archives-ouvertes.fr/hal-01193838

P. Crisp, D. Ganguly, S. Eichten, J. Borevitz, and B. Pogson, Reconsidering plant memory: intersections between stress recovery, RNA turnover, and epigenetics. Sci. Adv, vol.2, issue.2, p.1501340, 2016.
DOI : 10.1126/sciadv.1501340

URL : http://doi.org/10.1126/sciadv.1501340

P. Cubas, C. Vincent, and E. Coen, An epigenetic mutation responsible for natural variation in floral symmetry, Nature, vol.401, issue.6749, pp.157-61, 1999.

T. Day and R. Bonduriansky, A Unified Approach to the Evolutionary Consequences of Genetic and Nongenetic Inheritance, The American Naturalist, vol.178, issue.2, pp.18-36, 2011.
DOI : 10.1086/660911

R. Dowen, M. Pelizzola, R. Schmitz, R. Lister, and J. Dowen, Widespread dynamic DNA methylation in response to biotic stress, Proceedings of the National Academy of Sciences, vol.109, issue.32, pp.2183-91, 2012.
DOI : 10.1073/pnas.1209329109

J. Du, L. Johnson, S. Jacobsen, and D. Patel, DNA methylation pathways and their crosstalk with histone methylation, Nature Reviews Molecular Cell Biology, vol.71, issue.9, pp.519-551, 2015.
DOI : 10.1038/nrm4043

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4672940

M. Dubin, P. Zhang, D. Meng, M. Remigereau, and E. Osborne, DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation, p.5255, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01162697

S. Durand, N. Bouché, P. Strand, E. Loudet, O. Camilleri et al., Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation, Current Biology, vol.22, issue.4, pp.326-357, 2012.
DOI : 10.1016/j.cub.2011.12.054

URL : https://hal.archives-ouvertes.fr/hal-00999980

S. Eichten, R. Briskine, J. Song, Q. Li, and R. Swanson-wagner, Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations, The Plant Cell, vol.25, issue.8, pp.2783-97, 2013.
DOI : 10.1105/tpc.113.114793

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784580

S. Eichten, N. Ellis, I. Makarevitch, C. Yeh, and J. Gent, Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons, PLoS Genetics, vol.12, issue.12, p.1003127, 2012.
DOI : 10.1371/journal.pgen.1003127.s014

S. Eichten, R. Swanson-wagner, J. Schnable, A. Waters, and P. Hermanson, Heritable epigenetic variation among maize inbreds Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components, PLOS Genet. El-shami M Genes Dev, vol.7, issue.21, pp.2539-2583, 2007.

N. Fedoroff, The heritable activation of cryptic suppressor-mutator elements by an active element, Genetics, vol.121, issue.3, pp.591-608, 1989.

N. Fedoroff, M. Schläppi, and R. R. , transposon, BioEssays, vol.238, issue.4, pp.291-97, 1995.
DOI : 10.1002/bies.950170405

R. Fujimoto, Y. Kinoshita, A. Kawabe, T. Kinoshita, and K. Takashima, Evolution and Control of Imprinted FWA Genes in the Genus Arabidopsis, PLoS Genetics, vol.26, issue.13, p.1000048, 2008.
DOI : 10.1371/journal.pgen.1000048.s009

Z. Gao, H. Liu, L. Daxinger, O. Pontes, and X. He, An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation, Nature, vol.297, issue.7294, pp.106-115, 2010.
DOI : 10.1038/nature09025

URL : https://hal.archives-ouvertes.fr/hal-00788419

M. Gehring, Genomic Imprinting: Insights From Plants, Annual Review of Genetics, vol.47, issue.1, pp.187-208, 2013.
DOI : 10.1146/annurev-genet-110711-155527

A. Gendrel and E. Heard, Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation, Annual Review of Cell and Developmental Biology, vol.30, issue.1, pp.561-80, 2014.
DOI : 10.1146/annurev-cellbio-101512-122415

J. Gent, N. Ellis, L. Guo, A. Harkess, and Y. Yao, CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize, Genome Research, vol.23, issue.4, pp.628-665, 2013.
DOI : 10.1101/gr.146985.112

J. Geoghegan and H. Spencer, Exploring epiallele stability in a population-epigenetic model, Theoretical Population Biology, vol.83, pp.136-180, 2013.
DOI : 10.1016/j.tpb.2012.09.001

J. Geoghegan and H. Spencer, The adaptive invasion of epialleles in a heterogeneous environment, Theoretical Population Biology, vol.88, 2013.
DOI : 10.1016/j.tpb.2013.05.001

J. Geoghegan and H. Spencer, The evolutionary potential of paramutation: A population-epigenetic model, Theoretical Population Biology, vol.88, pp.9-19, 2013.
DOI : 10.1016/j.tpb.2013.05.003

A. Gilly, M. Etcheverry, M. Madoui, J. Guy, and L. Quadrana, TE-Tracker: systematic identification of transposition events through whole-genome resequencing, BMC Bioinformatics, vol.21, issue.6, p.377, 2014.
DOI : 10.1186/s12859-014-0377-z

URL : http://doi.org/10.1186/s12859-014-0377-z

J. Hagmann, C. Becker, M. ¨. , J. Stegle, O. Meyer et al., Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage, PLoS Genetics, vol.9, issue.1, p.1004920, 2015.
DOI : 10.1371/journal.pgen.1004920.s036

URL : http://hdl.handle.net/11858/00-001M-0000-0025-74F9-E

E. Heard and R. Martienssen, Transgenerational Epigenetic Inheritance: Myths and Mechanisms, Cell, vol.157, issue.1, pp.95-109, 2014.
DOI : 10.1016/j.cell.2014.02.045

L. Holeski, G. Jander, and A. Agrawal, Transgenerational defense induction and epigenetic inheritance in plants, Trends in Ecology & Evolution, vol.27, issue.11, pp.618-644, 2012.
DOI : 10.1016/j.tree.2012.07.011

R. Holliday, The inheritance of epigenetic defects, Science, vol.238, issue.4824, pp.163-70, 1987.
DOI : 10.1126/science.3310230

J. Hollister and B. Gaut, Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression, Genome Research, vol.19, issue.8, pp.1419-1447, 2009.
DOI : 10.1101/gr.091678.109

T. Hsieh, C. Ibarra, P. Silva, A. Zemach, and L. Eshed-williams, Genome-Wide Demethylation of Arabidopsis Endosperm, Science, vol.324, issue.5933, pp.1451-54, 2009.
DOI : 10.1126/science.1172417

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190

C. Ibarra, X. Feng, V. Schoft, T. Hsieh, and R. Uzawa, Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes, Science, vol.337, issue.6100, pp.1360-64, 2012.
DOI : 10.1126/science.1224839

S. Inagaki, A. Miura-kamio, Y. Nakamura, F. Lu, and X. Cui, Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome, The EMBO Journal, vol.39, issue.20, pp.3496-3506, 2010.
DOI : 10.1038/emboj.2010.227

T. Ito, Y. Tarutani, T. To, M. Kassam, and E. Duvernois-berthet, Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis, PLOS Genetics, vol.104, issue.4, p.1005154, 2015.
DOI : 10.1371/journal.pgen.1005154.s029

M. Iwasaki and J. Paszkowski, Identification of genes preventing transgenerational transmission of stress-induced epigenetic states, Proceedings of the National Academy of Sciences, vol.111, issue.23, pp.8547-52, 2014.
DOI : 10.1073/pnas.1402275111

E. Jablonka and M. Lamb, The inheritance of acquired epigenetic variations, Journal of Theoretical Biology, vol.139, issue.1, pp.1094-103, 1989.
DOI : 10.1016/S0022-5193(89)80058-X

C. Jiang, A. Mithani, E. Belfield, R. Mott, L. Hurst et al., mutations and epimutations, Genome Research, vol.50, issue.11, pp.1821-1850, 2014.
DOI : 10.1038/ng1929

F. Johannes and M. Colomé-tatché, Concerning epigenetics and inbreeding, Nature Reviews Genetics, vol.11, issue.5, p.376, 2011.
DOI : 10.1038/nrg2664-c3

F. Johannes, V. Colot, and R. Jansen, Epigenome dynamics: a quantitative genetics perspective, Nature Reviews Genetics, vol.128, issue.11, pp.883-90, 2008.
DOI : 10.1038/nrg2467

F. Johannes, E. Porcher, F. Teixeira, V. Saliba-colombani, and J. Albuisson, Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits, PLoS Genetics, vol.270, issue.6, p.38, 2009.
DOI : 10.1371/journal.pgen.1000530.s007

URL : https://hal.archives-ouvertes.fr/hal-01193366

L. Johnson, J. Du, C. Hale, S. Bischof, and S. Feng, Corrigendum: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation, Nature, vol.507, issue.7643, pp.124-152, 2014.
DOI : 10.1038/nature21398

P. Jullien, D. Susaki, R. Yelagandula, T. Higashiyama, and F. Berger, DNA Methylation Dynamics during Sexual Reproduction in Arabidopsis thaliana, Current Biology, vol.22, issue.19, pp.1825-1855, 2012.
DOI : 10.1016/j.cub.2012.07.061

M. Kankel, D. Ramsey, T. Stokes, S. Flowers, and J. Haag, Arabidopsis MET1 cytosine methyltransferase mutants, Genetics, vol.163, issue.3, pp.1109-1131, 2003.

T. Kanno, M. Mette, D. Kreil, W. Aufsatz, M. Matzke et al., Involvement of Putative SNF2 Chromatin Remodeling Protein DRD1 in RNA-Directed DNA Methylation, Current Biology, vol.14, issue.9, pp.801-806, 2004.
DOI : 10.1016/j.cub.2004.04.037

T. Kawakatsu, S. Huang, F. Jupe, E. Sasaki, and R. Schmitz, Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions, Cell, vol.166, issue.2, pp.492-505, 2016.
DOI : 10.1016/j.cell.2016.06.044

T. Kawashima and F. Berger, Epigenetic reprogramming in plant sexual reproduction, Nature Reviews Genetics, vol.13, issue.9, pp.613-637, 2014.
DOI : 10.1038/nrg3503

R. Kohli and Y. Zhang, TET enzymes, TDG and the dynamics of DNA demethylation, Nature, vol.502, issue.7472, pp.472-79, 2013.
DOI : 10.1016/j.cell.2012.11.022

I. Kronholm and S. Collins, Epigenetic mutations can both help and hinder adaptive evolution, Molecular Ecology, vol.2, issue.8, pp.1856-68, 2015.
DOI : 10.1111/mec.13296

V. Latzel, E. Allan, B. Silveira, A. Colot, V. Fischer et al., Epigenetic diversity increases the productivity and stability of plant populations, Nature Communications, vol.468, p.2875, 2013.
DOI : 10.1038/ncomms3875

J. Law, I. Ausin, L. Johnson, A. Vashisht, and J. Zhu, A Protein Complex Required for Polymerase V Transcripts and RNA- Directed DNA Methylation in Arabidopsis, Current Biology, vol.20, issue.10, pp.951-56, 2010.
DOI : 10.1016/j.cub.2010.03.062

J. Law, J. Du, C. Hale, S. Feng, and K. Krajewski, Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1, Nature, vol.20, issue.7454, pp.385-89, 2013.
DOI : 10.1038/nature12178

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119789

J. Law and S. Jacobsen, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nature Reviews Genetics, vol.28, issue.3, pp.204-224, 2010.
DOI : 10.1038/nrg2719

C. Li, O. Pontes, M. El-shami, I. Henderson, and Y. Bernatavichute, An ARGONAUTE4-Containing Nuclear Processing Center Colocalized with Cajal Bodies in Arabidopsis thaliana, Cell, vol.126, issue.1, pp.93-106, 2006.
DOI : 10.1016/j.cell.2006.05.032

URL : https://hal.archives-ouvertes.fr/hal-00164266

Q. Li, S. Eichten, P. Hermanson, and N. Springer, Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines, Genetics, vol.196, issue.3, pp.667-76, 2014.
DOI : 10.1534/genetics.113.158980

X. Li, J. Zhu, F. Hu, S. Ge, and M. Ye, Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression, BMC Genomics, vol.13, issue.1, p.300, 2012.
DOI : 10.1093/molbev/msm092

Z. Lippman, A. Gendrel, M. Black, M. Vaughn, and N. Dedhia, Role of transposable elements in heterochromatin and epigenetic control, Nature, vol.88, issue.6998, pp.471-76, 2004.
DOI : 10.1198/1085711031256

R. Lister, R. Malley, J. Tonti-filippini, B. Gregory, and C. Berry, Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis, Cell, vol.133, issue.3, pp.523-559, 2008.
DOI : 10.1016/j.cell.2008.03.029

Q. Long, F. Rabanal, D. Meng, C. Huber, and A. Farlow, Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden, Nature Genetics, vol.162, issue.8, pp.45884-90, 2013.
DOI : 10.1038/nature06250

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755268

L. Sánchez, A. Stassen, J. Furci, L. Smith, L. Ton et al., The role of DNA (de)methylation in immune responsiveness of Arabidopsis, Plant J. In press, 2016.

E. Luna, T. Bruce, M. Roberts, V. Flors, and J. Ton, Next-Generation Systemic Acquired Resistance, PLANT PHYSIOLOGY, vol.158, issue.2, pp.844-53, 2012.
DOI : 10.1104/pp.111.187468

K. Manning, T. ¨. , M. Poole, M. Hong, Y. Thompson et al., A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening, Nature Genetics, vol.14, issue.8, pp.38948-52, 2006.
DOI : 10.1093/bioinformatics/18.11.1427

A. Marí-ordóñezord´ordóordó?ordóñez, A. Marchais, M. Etcheverry, A. Martin, V. Colot et al., Reconstructing de novo silencing of an active plant retrotransposon, Nature Genetics, vol.38, issue.9, pp.1029-1068, 2013.
DOI : 10.1093/bioinformatics/btq033

R. Martienssen, Transposons, DNA methylation and gene control, Trends in Genetics, vol.14, issue.7, pp.263-64, 1998.
DOI : 10.1016/S0168-9525(98)01518-2

R. Martienssen and V. Colot, DNA Methylation and Epigenetic Inheritance in Plants and Filamentous Fungi, Science, vol.293, issue.5532, pp.1070-7438, 2001.
DOI : 10.1126/science.293.5532.1070

A. Martin, C. Troadec, A. Boualem, M. Rajab, and R. Fernandez, A transposon-induced epigenetic change leads to sex determination in melon, Nature, vol.25, issue.7267, pp.1135-1173, 2009.
DOI : 10.1038/nature08498

URL : https://hal.archives-ouvertes.fr/hal-01203855

O. Mathieu, J. Reinders, M. Caikovski, C. Smathajitt, and J. Paszkowski, Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation, Cell, vol.130, issue.5, pp.851-62, 2007.
DOI : 10.1016/j.cell.2007.07.007

M. Matzke and R. Mosher, RNA-directed DNA methylation: an epigenetic pathway of increasing complexity, Nature Reviews Genetics, vol.15, issue.6, pp.394-408, 2014.
DOI : 10.1534/genetics.110.125401

B. Mcclintock, The control of gene action in maize, Brookhaven Symp. Biol, vol.18, pp.162-84, 1965.

A. Mccue, S. Nuthikattu, S. Reeder, and R. Slotkin, Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA, PLoS Genetics, vol.428, issue.2, p.1002474, 2012.
DOI : 10.1371/journal.pgen.1002474.s008

A. Mccue, K. Panda, S. Nuthikattu, S. Choudury, E. Thomas et al., ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation, The EMBO Journal, vol.34, issue.1, pp.20-35, 2015.
DOI : 10.15252/embj.201489499

D. Meng, M. Dubin, P. Zhang, E. Osborne, and O. Stegle, Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana, PLOS Genetics, vol.38, issue.8, p.1006141, 2016.
DOI : 10.1371/journal.pgen.1006141.s013

M. Mirouze, J. Reinders, E. Bucher, T. Nishimura, and K. Schneeberger, Selective epigenetic control of retrotransposition in Arabidopsis, Nature, vol.408, issue.7262, pp.427-457, 2009.
DOI : 10.1038/nature08328

A. Miura, S. Yonebayashi, K. Watanabe, T. Toyama, H. Shimada et al., Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis, Nature, vol.15, issue.6834, pp.212-226, 2001.
DOI : 10.1038/35075612

K. Miura, M. Agetsuma, H. Kitano, A. Yoshimura, and M. Matsuoka, A metastable DWARF1 epigenetic mutant affecting plant stature in rice, Proceedings of the National Academy of Sciences, vol.106, issue.27, pp.11218-11241, 2009.
DOI : 10.1073/pnas.0901942106

R. Mosher, C. Melnyk, K. Kelly, R. Dunn, D. Studholme et al., Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis, Nature, vol.136, issue.7252, pp.283-86, 2009.
DOI : 10.1038/nature08084

K. Myant and I. Stancheva, LSH Cooperates with DNA Methyltransferases To Repress Transcription, Molecular and Cellular Biology, vol.28, issue.1, pp.215-241, 2008.
DOI : 10.1128/MCB.01073-07

C. Niederhuth, A. Bewick, J. L. Alabady, M. , D. Kim et al., Widespread natural variation of DNA methylation within angiosperms, 2015.

S. Nuthikattu, A. Mccue, K. Panda, D. Fultz, and C. Defraia, The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs, PLANT PHYSIOLOGY, vol.162, issue.1, pp.116-147, 2013.
DOI : 10.1104/pp.113.216481

M. Ong-abdullah, J. Ordway, N. Jiang, S. Ooi, and S. Kok, Loss of Karma transposon methylation underlies the??mantled somaclonal variant of oil palm, Nature, vol.108, issue.7570, pp.533-570, 2015.
DOI : 10.1038/nature15365

S. Ossowski, K. Schneeberger, J. Lucas-lledólled´lledó, N. Warthmann, and R. Clark, The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana, Science, vol.327, issue.5961, pp.92-94, 2010.
DOI : 10.1126/science.1180677

C. Pál, Plasticity, memory and the adaptive landscape of the genotype, Proceedings of the Royal Society B: Biological Sciences, vol.265, issue.1403, pp.1319-1342, 1403.
DOI : 10.1098/rspb.1998.0436

C. Pál, M. , and I. , Epigenetic Inheritance, Genetic Assimilation and Speciation, Journal of Theoretical Biology, vol.200, issue.1, pp.19-37, 1999.
DOI : 10.1006/jtbi.1999.0974

J. Penterman, D. Zilberman, J. Huh, T. Ballinger, S. Henikoff et al., DNA demethylation in the Arabidopsis genome, Proceedings of the National Academy of Sciences, vol.104, issue.16, pp.6752-57, 2007.
DOI : 10.1073/pnas.0701861104

D. Pontier, C. Picart, F. Roudier, D. Garcia, and S. Lahmy, NERD, a Plant-Specific GW Protein, Defines an Additional RNAi-Dependent Chromatin-Based Pathway in Arabidopsis, Molecular Cell, vol.48, issue.1, pp.121-153, 2012.
DOI : 10.1016/j.molcel.2012.07.027

URL : https://hal.archives-ouvertes.fr/hal-00742627

L. Quadrana, J. Almeida, R. Asís, T. Duffy, and P. Dominguez, Natural occurring epialleles determine vitamin E accumulation in tomato fruits, Nature Communications, vol.25, p.3027, 2014.
DOI : 10.1186/1746-4811-1-14

URL : http://doi.org/10.1038/ncomms5027

L. Quadrana, A. Silveira, G. Mayhew, C. Leblanc, and R. Martienssen, The Arabidopsis thaliana mobilome and its impact at the species level. eLife, pp.1-25, 2016.

M. Regulski, Z. Lu, J. Kendall, M. Donoghue, and J. Reinders, The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA, Genome Research, vol.23, issue.10, pp.1651-62, 2013.
DOI : 10.1101/gr.153510.112

J. Reinders, B. Wulff, M. Mirouze, M. Nez, A. Dapp et al., Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes, Genes & Development, vol.23, issue.8, pp.939-50, 2009.
DOI : 10.1101/gad.524609

E. Richards, Inherited epigenetic variation ??? revisiting soft inheritance, Nature Reviews Genetics, vol.17, issue.5, pp.395-401, 2006.
DOI : 10.1038/nrg1834

N. Riddle and E. Richards, The control of natural variation in cytosine methylation in Arabidopsis, Genetics, vol.162, issue.1, pp.355-63, 2002.

M. Rigal, C. Becker, T. Pélissier, R. Pogorelcnik, and J. Devos, F1 epihybrids, Proceedings of the National Academy of Sciences, vol.113, issue.14, pp.2083-92, 2016.
DOI : 10.1073/pnas.1600672113

M. Rigal, Z. Kevei, T. Pélissier, and O. Mathieu, DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns, The EMBO Journal, vol.39, issue.13, pp.312981-93, 2012.
DOI : 10.1038/emboj.2012.141

A. Riggs, X inactivation, differentiation, and DNA methylation, Cytogenetic and Genome Research, vol.14, issue.1, pp.9-25, 1975.
DOI : 10.1159/000130315

F. Roux, M. Colomé-tatché, C. Edelist, R. Wardenaar, and P. Guerche, Genome-Wide Epigenetic Perturbation Jump-Starts Patterns of Heritable Variation Found in Nature, Genetics, vol.188, issue.4, pp.1015-1032, 2011.
DOI : 10.1534/genetics.111.128744

URL : https://hal.archives-ouvertes.fr/hal-00604163

H. Saze, A. Shiraishi, A. Miura, and T. Kakutani, Control of Genic DNA Methylation by a jmjC Domain-Containing Protein in Arabidopsis thaliana, Science, vol.319, issue.5862, pp.462-65, 2008.
DOI : 10.1126/science.1150987

R. Schmitz, Y. He, O. Valdes-lopez, S. Khan, and T. Joshi, Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population, Genome Research, vol.23, issue.10, pp.1663-74, 2013.
DOI : 10.1101/gr.152538.112

R. Schmitz, M. Schultz, M. Lewsey, O. Malley, R. Urich et al., Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants, Science, vol.334, issue.6054, pp.369-73, 2011.
DOI : 10.1126/science.1212959

R. Schmitz, M. Schultz, M. Urich, J. Nery, and M. Pelizzola, Patterns of population epigenomic diversity, Nature, vol.495, issue.7440, pp.193-98, 2013.
DOI : 10.1371/journal.pgen.1000232

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798000

D. Secco, C. Wang, H. Shou, M. Schultz, and S. Chiarenza, http://dx.doi.org/10.7554/eLife.09343.036, eLife, vol.31, pp.1-26, 2015.
DOI : 10.7554/eLife.09343.036

S. Seisenberger, J. Peat, T. Hore, F. Santos, W. Dean et al., Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.139, issue.19, p.20110330, 1609.
DOI : 10.1242/dev.081661

D. Seymour, D. Koenig, J. Hagmann, C. Becker, and D. Weigel, Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization, PLoS Genetics, vol.19, issue.11, p.1004785, 2014.
DOI : 10.1371/journal.pgen.1004785.s035

X. Shen, D. Jonge, J. Forsberg, S. Pettersson, M. Sheng et al., Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality, PLoS Genetics, vol.301, issue.12, p.1004842, 2014.
DOI : 10.1371/journal.pgen.1004842.s051

A. Silveira, C. Trontin, S. Cortijo, J. Barau, D. Bem et al., Extensive Natural Epigenetic Variation at a De Novo Originated Gene, PLoS Genetics, vol.39, issue.4, p.1003437, 2013.
DOI : 10.1371/journal.pgen.1003437.s005

URL : https://hal.archives-ouvertes.fr/hal-01190576

T. Singer, C. Yordan, and R. Martienssen, Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1), Genes & Development, vol.15, issue.5, pp.591-602, 2001.
DOI : 10.1101/gad.193701

R. Slotkin, M. Vaughn, F. Borges, M. Tanurd?i´tanurd?i´c, and J. Becker, Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen, Cell, vol.136, issue.3, pp.461-72, 2009.
DOI : 10.1016/j.cell.2008.12.038

S. Stelpflug, S. Eichten, P. Hermanson, N. Springer, and S. Kaeppler, Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize, Genetics, vol.198, issue.1, pp.209-227, 2014.
DOI : 10.1534/genetics.114.165480

H. Stroud, B. Ding, S. Simon, S. Feng, and M. Bellizzi, Figure 6???figure supplement 1. Callus induced CHH hypermethylation., eLife, vol.19, p.354, 2013.
DOI : 10.7554/eLife.00354.018

H. Stroud, T. Do, J. Du, X. Zhong, and S. Feng, Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis, Nature Structural & Molecular Biology, vol.733, issue.1, pp.64-72, 2014.
DOI : 10.1126/science.1221472

H. Stroud, M. Greenberg, S. Feng, Y. Bernatavichute, and S. Jacobsen, Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome, Cell, vol.152, issue.1-2, pp.352-64, 2013.
DOI : 10.1016/j.cell.2012.10.054

S. Takuno and B. Gaut, Gene body methylation is conserved between plant orthologs and is of evolutionary consequence, Proceedings of the National Academy of Sciences, vol.110, issue.5, pp.1797-802, 2013.
DOI : 10.1073/pnas.1215380110

S. Takuno, J. Ran, and B. Gaut, Evolutionary patterns of genic DNA methylation vary across land plants, Nature Plants, vol.342, issue.2, p.15222, 2016.
DOI : 10.1093/nar/gki107

M. Tanurdzic, M. Vaughn, H. Jiang, T. Lee, and R. Slotkin, Epigenomic Consequences of Immortalized Plant Cell Suspension Culture, PLoS Biology, vol.57, issue.12, pp.2880-95, 2008.
DOI : 10.1371/journal.pbio.0060302.sd001

F. Teixeira and V. Colot, Gene body DNA methylation in plants: a means to an end or an end to a means?, The EMBO Journal, vol.28, issue.8, pp.997-9838, 2009.
DOI : 10.1038/ng1929

F. Teixeira, F. Heredia, A. Sarazin, F. Roudier, and M. Boccara, A Role for RNAi in the Selective Correction of DNA Methylation Defects, Science, vol.323, issue.5921, pp.1600-1604, 2009.
DOI : 10.1126/science.1165313

URL : https://hal.archives-ouvertes.fr/hal-00400271

P. Thakore, J. Black, I. Hilton, and C. Gersbach, Editing the epigenome: technologies for programmable transcription and epigenetic modulation, Nature Methods, vol.312, issue.2, pp.127-164, 2016.
DOI : 10.1172/JCI77321

S. Tsukahara, A. Kobayashi, A. Kawabe, O. Mathieu, A. Miura et al., Bursts of retrotransposition reproduced in Arabidopsis, Nature, vol.24, issue.7262, pp.423-449, 2009.
DOI : 10.1038/nature08351

A. Van-der-graaf, R. Wardenaar, D. Neumann, A. Taudt, and R. Shaw, Rate, spectrum, and evolutionary dynamics of spontaneous epimutations, Proceedings of the National Academy of Sciences, vol.112, issue.21, pp.6676-81, 2015.
DOI : 10.1073/pnas.1424254112

M. Vaughn, M. Tanurdzi´ctanurdzi´c, Z. Lippman, H. Jiang, and R. Carrasquillo, Epigenetic Natural Variation in Arabidopsis thaliana, PLoS Biology, vol.11, issue.7, p.174, 2007.
DOI : 10.1371/journal.pbio.0050174.st009

K. Verhoeven and T. Van-gurp, Transgenerational Effects of Stress Exposure on Offspring Phenotypes in Apomictic Dandelion, PLoS ONE, vol.57, issue.1, p.38605, 2012.
DOI : 10.1371/journal.pone.0038605.t004

K. Vining, K. Pomraning, L. Wilhelm, H. Priest, and M. Pellegrini, Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression, BMC Genomics, vol.13, issue.1, p.27, 2012.
DOI : 10.1186/gb-2010-11-10-r106

A. Vojta, P. Dobrini´cdobrini´c, V. Tadi´ctadi´c, L. Bo?kor, and P. Kora´ckora´c, Repurposing the CRISPR-Cas9 system for targeted DNA methylation, Nucleic Acids Research, vol.44, issue.12, pp.5615-5643, 2016.
DOI : 10.1093/nar/gkw159

A. Vongs, T. Kakutani, R. Martienssen, and E. Richards, Arabidopsis thaliana DNA methylation mutants, Science, vol.260, issue.5116, pp.1926-1954, 1993.
DOI : 10.1126/science.8316832

C. Waddington, Canalization of Development and the Inheritance of Acquired Characters, Nature, vol.150, issue.3811, pp.563-65, 1942.
DOI : 10.1038/150563a0

D. Weigel and V. Colot, Epialleles in plant evolution, Genome Biology, vol.13, issue.10, p.249, 2012.
DOI : 10.1080/10409230701648502

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491404

D. Weigel and M. Nordborg, Population Genomics for Understanding Adaptation in Wild Plant Species, Annual Review of Genetics, vol.49, issue.1, pp.315-353, 2015.
DOI : 10.1146/annurev-genet-120213-092110

A. Wibowo, C. Becker, G. Marconi, J. Durr, and J. Price, Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. eLife, p.13546, 2016.

E. Willing, V. Rawat, T. Mandáková, F. Maumus, and G. James, Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation, Nature Plants, vol.461, issue.2, p.14023, 2015.
DOI : 10.1038/nplants.2014.23

URL : https://hal.archives-ouvertes.fr/hal-01179557

H. Woo and E. Richards, Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana, BMC Plant Biology, vol.8, issue.1, pp.1-12, 2008.
DOI : 10.1186/1471-2229-8-92

D. Yang, G. Zhang, K. Tang, J. Li, and L. Yang, Dicer-independent RNA-directed DNA methylation in Arabidopsis, Cell Research, vol.26, issue.1, pp.66-82, 2016.
DOI : 10.1038/cr.2015.145

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816133

R. Ye, Z. Chen, B. Lian, M. Rowley, and N. Xia, A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis, Molecular Cell, vol.61, issue.2, pp.222-257, 2015.
DOI : 10.1016/j.molcel.2015.11.015

H. Yi, N. Riddle, T. Stokes, H. Woo, and E. Richards, Induced and Natural Epigenetic Variation, Cold Spring Harbor Symposia on Quantitative Biology, vol.7, issue.0, pp.155-60, 2004.
DOI : 10.1105/tpc.020479

A. Yu, G. Lepère, F. Jay, J. Wang, and L. Bapaume, Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense, Proceedings of the National Academy of Sciences, vol.110, issue.6, pp.2389-94, 2013.
DOI : 10.1073/pnas.1211757110

URL : https://hal.archives-ouvertes.fr/hal-00790051

A. Zemach, M. Kim, P. Hsieh, D. Coleman-derr, and L. Eshed-williams, The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin, Cell, vol.153, issue.1, pp.193-205, 2013.
DOI : 10.1016/j.cell.2013.02.033

URL : http://doi.org/10.1016/j.cell.2013.02.033

A. Zemach, I. Mcdaniel, P. Silva, and D. Zilberman, Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation, Science, vol.328, issue.5980, pp.916-935, 2010.
DOI : 10.1126/science.1186366

J. Zhai, S. Bischof, H. Wang, S. Feng, and T. Lee, A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis, Cell, vol.163, issue.2, pp.445-55, 2015.
DOI : 10.1016/j.cell.2015.09.032

X. Zhang, J. Yazaki, A. Sundaresan, S. Cokus, and S. Chan, Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis, Cell, vol.126, issue.6, pp.1189-201, 2006.
DOI : 10.1016/j.cell.2006.08.003

Y. Zhang, M. Fischer, V. Colot, and O. Bossdorf, Epigenetic variation creates potential for evolution of plant phenotypic plasticity, New Phytologist, vol.25, issue.1, pp.314-336, 2013.
DOI : 10.1111/nph.12010

B. Zheng, Z. Wang, S. Li, Y. B. Liu, J. Chen et al., Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis, Genes & Development, vol.23, issue.24, pp.2850-6038, 2009.
DOI : 10.1101/gad.1868009

S. Zhong, Z. Fei, Y. Chen, Y. Zheng, and M. Huang, Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening, Nature Biotechnology, vol.57, issue.2, pp.31154-59, 2013.
DOI : 10.1186/gb-2008-9-9-r137

D. Zilberman, M. Gehring, R. Tran, T. Ballinger, and S. Henikoff, Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription, Nature Genetics, vol.10, issue.1, pp.61-69, 2006.
DOI : 10.1038/ng1929

X. Zhong, J. Du, C. Hale, J. Gallego-bartolome, and S. Feng, Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases, Cell, vol.157, issue.5, pp.1050-6049, 2014.
DOI : 10.1016/j.cell.2014.03.056

S. Sex-biased-gene-expression, J. Grath, D. Parsch-lauren, and E. P. Palmer, Sperm Meets Egg: The Genetics of Mammalian Fertilization Enrica Bianchi and Gavin J, p93 Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes J. Chris Pires and Gavin C, pp.67-113

. Control-of-meiotic-crossovers-stephen, P. E. Gray, and . Cohen, From Double-Stand Break Formation to Designation, p.175

B. Daniel, C. Vogel, Y. Bai, and J. A. , The Plant Microbiota: Systems-Level Insights and Perspectives, p.211

H. Wu, S. Wang, X. Ling, and . Lu, The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process, Annual Review of Genetics, vol.50, issue.1, p.347
DOI : 10.1146/annurev-genet-112414-054842

H. Vaccination-via-chloroplast-genetics-daniell and E. K. Chan, Affordable Protein Drugs for the Prevention and Treatment of Inherited or Infectious Human Diseases Henry, p.595