X. Adenot, T. Elmayan, D. Lauressergues, S. Boutet, N. Bouché et al., DRB4-Dependent TAS3 trans-Acting siRNAs Control Leaf Morphology through AGO7, Current Biology, vol.16, issue.9, pp.927-932, 2006.
DOI : 10.1016/j.cub.2006.03.035

URL : https://doi.org/10.1016/j.cub.2006.03.035

P. Amedeo, Y. Habu, K. Afsar, O. M. Scheid, and J. Paszkowski, Disruption of the plant gene MOM releases transcriptional silencing of methylated genes, Nature, vol.12, issue.6783, pp.203-206, 2000.
DOI : 10.1046/j.1365-313X.1997.12040945.x

L. Arribas-hernández, L. J. Kielpinski, and P. Brodersen, mRNA decay of most Arabidopsis miRNA targets requires slicer activity of AGO1, Plant Physiology, vol.171, pp.2620-2632, 2016.
DOI : 10.1104/pp.16.00231

K. Baeg, H. Iwakawa, and Y. Tomari, The poly(A) tail blocks RDR6 from converting self mRNAs into substrates for gene silencing, Nature Plants, vol.28, issue.4, pp.1-4, 2017.
DOI : 10.1016/j.cell.2008.02.033

D. Balciunas and H. Ronne, Evidence of domain swapping within the jumonji family of transcription factors, Trends in Biochemical Sciences, vol.25, issue.6, pp.274-276, 2000.
DOI : 10.1016/S0968-0004(00)01593-0

N. Baumberger and D. C. Baulcombe, Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs, Proceedings of the National Academy of Sciences, vol.278, issue.3, pp.11928-11933, 2005.
DOI : 10.1074/jbc.M208968200

URL : http://www.pnas.org/content/102/33/11928.full.pdf

A. Berr, S. Shafiq, and W. Shen, Histone modifications in transcriptional activation during plant development, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1809, issue.10, pp.567-576, 2011.
DOI : 10.1016/j.bbagrm.2011.07.001

URL : https://hal.archives-ouvertes.fr/hal-00631173

T. Blevins, R. Podicheti, V. Mishra, M. Marasco, J. Wang et al., Author response, eLife, vol.299, issue.80, p.9591, 2015.
DOI : 10.7554/eLife.09591.039

T. Blevins, R. Rajeswaran, P. V. Shivaprasad, D. Beknazariants, A. Si-ammour et al., Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing, Nucleic Acids Research, vol.34, issue.21, pp.6233-6246, 2006.
DOI : 10.1093/nar/gkl886

URL : https://academic.oup.com/nar/article-pdf/34/21/6233/11171889/gkl886.pdf

K. Bohmert, I. Camus, C. Bellini, D. Bouchez, M. Caboche et al., AGO1 defines a novel locus of Arabidopsis controlling leaf development, The EMBO Journal, vol.17, issue.1, pp.170-180, 1998.
DOI : 10.1093/emboj/17.1.170

O. Borsani, J. Zhu, P. E. Verslues, R. Sunkar, and J. Zhu, Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis, Cell, vol.123, issue.7, p.1279, 2005.
DOI : 10.1016/j.cell.2005.11.035

N. Bouché, D. Lauressergues, V. Gasciolli, and H. Vaucheret, An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs, The EMBO Journal, vol.19, issue.14, p.3347, 2006.
DOI : 10.1038/sj.emboj.7601217

S. Boutet, F. Vazquez, J. Liu, C. Béclin, M. Fagard et al., Arabidopsis HEN1, Current Biology, vol.13, issue.10, pp.843-848, 2003.
DOI : 10.1016/S0960-9822(03)00293-8

URL : https://doi.org/10.1016/s0960-9822(03)00293-8

P. Brodersen, L. Sakvarelidze-achard, M. Bruun-rasmussen, P. Dunoyer, Y. Y. Yamamoto et al., Widespread Translational Inhibition by Plant miRNAs and siRNAs, Science, vol.12, issue.7, pp.1185-1190, 2008.
DOI : 10.1016/j.tplants.2007.05.001

C. A. Brosnan, N. Mitter, M. Christie, N. A. Smith, P. M. Waterhouse et al., Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis, Proceedings of the National Academy of Sciences, pp.14741-14746, 2007.
DOI : 10.1046/j.1365-313X.1993.t01-26-00999.x

C. Brosseau and P. Moffett, Functional and Genetic Analysis Identify a Role for Arabidopsis ARGONAUTE5 in Antiviral RNA Silencing, The Plant Cell, vol.27, issue.6, pp.1742-1754, 2015.
DOI : 10.1105/tpc.15.00264

N. Butel, L. Masson, I. Bouteiller, N. Vaucheret, H. Elmayan et al., downregulation, The Plant Journal, vol.348, issue.3, pp.509-519, 2017.
DOI : 10.1126/science.aaa2618

URL : https://hal.archives-ouvertes.fr/hal-01602624

X. Cao and S. E. Jacobsen, Role of the Arabidopsis DRM Methyltransferases in De Novo DNA Methylation and Gene Silencing, Current Biology, vol.12, issue.13, pp.1138-1144, 2002.
DOI : 10.1016/S0960-9822(02)00925-9

E. J. Chapman and J. C. Carrington, Specialization and evolution of endogenous small RNA pathways, Nature Reviews Genetics, vol.50, issue.11, pp.884-896, 2007.
DOI : 10.1016/j.cub.2004.01.035

P. Chellappan, R. Vanitharani, and C. M. Fauquet, Short Interfering RNA Accumulation Correlates with Host Recovery in DNA Virus-Infected Hosts, and Gene Silencing Targets Specific Viral Sequences, Journal of Virology, vol.78, issue.14, pp.7465-7477, 2004.
DOI : 10.1128/JVI.78.14.7465-7477.2004

URL : http://jvi.asm.org/content/80/2/1064.full.pdf

H. M. Chen, L. T. Chen, K. Patel, Y. H. Li, D. C. Baulcombe et al., 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants, Proceedings of the National Academy of Sciences, pp.15269-15274, 2010.
DOI : 10.1046/j.1365-313X.2003.01676.x

URL : http://www.pnas.org/content/107/34/15269.full.pdf

Y. Choi, M. Gehring, L. Johnson, M. Hannon, J. J. Harada et al., DEMETER, a DNA Glycosylase Domain Protein, Is Required for Endosperm Gene Imprinting and Seed Viability in Arabidopsis, Cell, vol.110, issue.1, pp.33-42, 2002.
DOI : 10.1016/S0092-8674(02)00807-3

S. J. Cokus, S. Feng, X. Zhang, Z. Chen, B. Merriman et al., Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature, vol.20, issue.7184, pp.215-219, 2008.
DOI : 10.1038/nature06745

K. M. Creasey, J. Zhai, F. Borges, F. Van-ex, M. Regulski et al., miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis, Nature, vol.25, issue.7496, pp.411-415, 2014.
DOI : 10.1101/gad.177527.111

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074602/pdf

T. Csorba, L. Kontra, and J. Burgyán, viral silencing suppressors: Tools forged to fine-tune host-pathogen coexistence, Virology, vol.479, issue.480, pp.479-480, 2015.
DOI : 10.1016/j.virol.2015.02.028

URL : https://doi.org/10.1016/j.virol.2015.02.028

D. Cuerda and R. K. Slotkin, Non-canonical RNA-directed DNA methylation, Nature Plants, vol.2, pp.1-8, 2016.

M. Gilbert, S. D. Montgomery, T. A. Carrington, and J. C. , Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis, 2010.

I. Furner, Unexpected silencing effects from T-DNA tags in Arabidopsis, Trends in Plant Science, vol.13, pp.4-8, 2008.

A. Deleris, J. Gallego-bartolome, J. Bao, K. D. Kasschau, J. C. Carrington et al., Hierarchical Action and Inhibition of Plant Dicer-Like Proteins in Antiviral Defense, Science, vol.313, issue.5783, pp.68-71, 2006.
DOI : 10.1038/sj.emboj.7601164

URL : https://hal.archives-ouvertes.fr/hal-00092877

A. Deleris, M. V. Greenberg, I. Ausin, R. W. Law, G. Moissiard et al., Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation, EMBO reports, vol.11, issue.12, pp.950-955, 2010.
DOI : 10.1186/gb-2009-10-6-r62

S. Deng, J. Xu, J. Liu, S. Kim, S. Shi et al., JMJ24 binds to RDR2 and is required for the basal level transcription of silenced loci in Arabidopsis, The Plant Journal, vol.22, issue.5, pp.770-782, 2015.
DOI : 10.1016/j.molcel.2006.05.010

Y. Ding, I. Ndamukong, Z. Xu, H. Lapko, M. Fromm et al., ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes, PLoS Genetics, vol.66, issue.12, p.1003111, 2012.
DOI : 10.1371/journal.pgen.1003111.s007

&. Guo and H. , DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene, The Plant Journal, vol.68, pp.633-645, 2011.

E. F. Dunn, Yeast poly(A)-binding protein, Pab1, and PAN, a poly(A) nuclease complex recruited by Pab1, connect mRNA biogenesis to export, Genes & Development, vol.19, issue.1, pp.90-103, 2005.
DOI : 10.1101/gad.1267005

P. Dunoyer, C. Himber, and O. Voinnet, DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal, Nature Genetics, vol.14, issue.12, p.1356, 2005.
DOI : 10.1038/ng1675

P. Dunoyer, C. Himber, V. Ruiz-ferrer, A. Alioua, and O. Voinnet, Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways, Nature Genetics, vol.82, issue.7, pp.848-856, 2007.
DOI : 10.1371/journal.pbio.0050057

S. Durand, N. Bouché, E. P. Strand, O. Loudet, and C. Camilleri, Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation, Current Biology, vol.22, issue.4, p.1, 2012.
DOI : 10.1016/j.cub.2011.12.054

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

N. Durán-figueroa and J. Vielle-calzada, ARGONAUTE9-dependent silencing of transposable elements in pericentromeric regions of Arabidopsis, Plant Signaling & Behavior, vol.5, issue.11, pp.1476-1479, 2010.
DOI : 10.1093/dnares/9.4.117

M. Duval, T. F. Hsieh, S. Y. Kim, and T. L. Thomas, Molecular characterization of AtNAM: a member of theArabidopsis NAC domain superfamily, Plant Molecular Biology, 2002.

S. Egloff and S. Murphy, Cracking the RNA polymerase II CTD code, Trends in Genetics, vol.24, issue.6, pp.280-288, 2008.
DOI : 10.1016/j.tig.2008.03.008

J. C. Palauqui, S. Vernhettes, T. Vialle, K. Wostrikoff, and H. Vaucheret, Arabidopsis mutants impaired in cosuppression, The Plant cell, vol.10, pp.1747-1758, 1998.

T. Elmayan, F. Proux, and H. Vaucheret, Arabidopsis RPA2: A Genetic Link among Transcriptional Gene Silencing, DNA Repair, and DNA Replication, Current Biology, vol.15, issue.21, pp.1919-1925, 2005.
DOI : 10.1016/j.cub.2005.09.044

URL : https://doi.org/10.1016/j.cub.2005.09.044

E. Elvira-matelot, F. Bardou, F. Ariel, V. Jauvion, N. Bouteiller et al., The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis. The Plant cell, vol.28, pp.426-438, 2016.
DOI : 10.1105/tpc.15.01045

URL : http://www.plantcell.org/content/plantcell/28/2/426.full.pdf

H. A. Ernst, A. N. Olsen, K. Skriver, S. Larsen, . Leggio et al., Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors, EMBO reports, vol.419, issue.3, pp.297-303, 2004.
DOI : 10.1038/nature00998

J. C. Carrington, Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis, Current Biology, vol.16, pp.939-944, 2006.

S. Feng, S. J. Cokus, X. Zhang, P. Y. Chen, M. Bostick et al., Conservation and divergence of methylation patterning in plants and animals, Proceedings of the National Academy of Sciences, pp.8689-8694, 2010.
DOI : 10.1080/00401706.1999.10485670

F. Fenselau-de-felippes, F. Ott, and D. Weigel, Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana, Nucleic Acids Research, vol.39, issue.7, p.2880, 2010.
DOI : 10.1093/nar/gkq1240

C. M. Fraser, An Expression and Bioinformatics Analysis of the Arabidopsis Serine Carboxypeptidase-Like Gene Family, PLANT PHYSIOLOGY, vol.138, issue.2, pp.1136-1148, 2005.
DOI : 10.1104/pp.104.057950

M. Fromm and Z. Avramova, ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes?, Current Opinion in Plant Biology, vol.21, pp.75-82, 2014.
DOI : 10.1016/j.pbi.2014.07.004

O. Garnier, V. Serrano, S. Duharcourt, and E. Meyer, RNA-Mediated Programming of Developmental Genome Rearrangements in Paramecium tetraurelia, Molecular and Cellular Biology, vol.24, issue.17, pp.7370-7379, 2004.
DOI : 10.1128/MCB.24.17.7370-7379.2004

A. V. Gendrel, Z. Lippman, C. Yordan, V. Colot, and R. A. Martienssen, Dependence of Heterochromatic Histone H3 Methylation Patterns on the Arabidopsis Gene DDM1, Science, vol.297, issue.5588, pp.1871-1873, 2002.
DOI : 10.1126/science.1074950

R. J. Grainger and J. D. Beggs, Prp8 protein: At the heart of the spliceosome, RNA, vol.11, issue.5, pp.533-557, 2005.
DOI : 10.1261/rna.2220705

I. Gy, V. Gasciolli, D. Lauressergues, J. B. Morel, J. Gombert et al., Arabidopsis FIERY1, XRN2, and XRN3 Are Endogenous RNA Silencing Suppressors, Arabidopsis FIERY1, XRN2, and XRN3 Are Endogenous RNA Silencing Suppressors, pp.3451-3461, 2007.
DOI : 10.1105/tpc.107.055319

URL : http://www.plantcell.org/content/plantcell/19/11/3451.full.pdf

Y. Habu, O. Mathieu, M. Tariq, A. V. Probst, C. Smathajitt et al., Epigenetic regulation of transcription in intermediate heterochromatin, EMBO reports, vol.19, issue.12, pp.1279-1284, 2006.
DOI : 10.1016/S0981-9428(00)01234-1

O. Hadjebi, E. Casas-terradellas, F. R. Garcia-gonzalo, and J. L. Rosa, The RCC1 superfamily: From genes, to function, to disease, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1783, issue.8, 2008.
DOI : 10.1016/j.bbamcr.2008.03.015

A. J. Hamilton, A Species of Small Antisense RNA in Posttranscriptional Gene Silencing in Plants, Science, vol.286, issue.5441, pp.950-952, 1999.
DOI : 10.1126/science.286.5441.950

Y. Han, Q. Zhao, L. Dang, Y. Luo, S. Chen et al., The SUMO E3 Ligase-Like Proteins PIAL1 and PIAL2 Interact with MOM1 and Form a Novel Complex Required for Transcriptional Silencing, The SUMO E3 Ligase-Like Proteins PIAL1 and PIAL2 Interact with MOM1 and Form a Novel Complex Required for Transcriptional Silencing, pp.1215-1229, 2016.
DOI : 10.1105/tpc.15.00997

J. J. Harvey, M. G. Lewsey, K. Patel, J. Westwood, S. Heimstädt et al., An Antiviral Defense Role of AGO2 in Plants, PLoS ONE, vol.6, issue.1, p.14639, 2011.
DOI : 10.1371/journal.pone.0014639.g004

T. Hebbes, A. Thorne, and C. Crane-robinson, A direct link between core histone acetylation and transcriptionally active chromatin, The EMBO journal, vol.7, pp.1395-1402, 1988.

I. R. Henderson, X. Zhang, C. Lu, L. Johnson, B. C. Meyers et al., Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning, Nature Genetics, vol.32, issue.6, pp.721-725, 2006.
DOI : 10.1093/nar/gnh171

I. Hernandez-pinzon, N. E. Yelina, F. Schwach, D. J. Studholme, D. Baulcombe et al., SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans-acting endogenous siRNA, The Plant Journal, vol.19, issue.1, pp.140-148, 2007.
DOI : 10.1016/S0022-2836(05)80360-2

C. Himber, P. Dunoyer, G. Moissiard, C. Ritzenthaler, and O. Voinnet, Transitivity-dependent and -independent cell-to-cell movement of RNA silencing, The EMBO Journal, vol.22, issue.17, 2003.
DOI : 10.1093/emboj/cdg431

D. Holoch and D. Moazed, RNA-mediated epigenetic regulation of gene expression, Nature Reviews Genetics, vol.16, issue.2, pp.71-84, 2015.
DOI : 10.1016/j.molcel.2013.08.046

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376354/pdf

E. Hong, Y. Jeong, J. Ryu, R. M. Amasino, B. Noh et al., Temporal and spatial expression patterns of nine Arabidopsis genes encoding Jumonji C-domain proteins, Molecules and Cells, vol.8, issue.4, pp.481-490, 2009.
DOI : 10.1007/s10059-009-0054-7

Y. W. Iwasaki, M. C. Siomi, and H. Siomi, PIWI-Interacting RNA: Its Biogenesis and Functions, Annual Review of Biochemistry, vol.84, issue.1, pp.405-433, 2015.
DOI : 10.1146/annurev-biochem-060614-034258

V. Jauvion, Analyse de mutants de RNAi chez Arabidopsis thaliana thèse de biologie végétale, encadré par Vaucheret, 2010.

V. Jauvion, T. Elmayan, and H. Vaucheret, The Conserved RNA Trafficking Proteins HPR1 and TEX1 Are Involved in the Production of Endogenous and Exogenous Small Interfering RNA in Arabidopsis, The Plant Cell, vol.22, issue.8, pp.2697-2709, 2010.
DOI : 10.1105/tpc.110.076638

URL : https://hal.archives-ouvertes.fr/hal-01203899

J. A. Jeddeloh, T. L. Stokes, and E. J. Richards, Maintenance of genomic methylation requires a SWI2/SNF2-like protein, Nature Genetics, vol.22, pp.94-97, 1999.

R. A. Jefferson, T. A. Kavanagh, and M. W. Bevan, GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants, The EMBO journal, vol.6, pp.3901-3907, 1987.

M. K. Jensen, T. Kjaersgaard, M. M. Nielsen, P. Galberg, K. Petersen et al., NAC transcription factor family: structure???function relationships and determinants of ANAC019 stress signalling, Biochemical Journal, vol.106, issue.2, pp.183-196, 2010.
DOI : 10.1111/j.1365-313X.2004.02238.x

&. Noh and Y. , Repression of FLOWERING LOCUS T Chromatin by Functionally Redundant Histone H3 Lysine 4 Demethylases in Arabidopsis, PLoS ONE, vol.4, p.8033, 2009.

C. Verbsky, M. L. Richards, and E. J. , Arabidopsis MET1 cytosine methyltransferase mutants, Genetics, vol.163, pp.1109-1122, 2003.

T. Kanno, M. F. Mette, D. P. Kreil, W. Aufsatz, and M. Matzke, Involvement of Putative SNF2 Chromatin Remodeling Protein DRD1 in RNA-Directed DNA Methylation, Current Biology, vol.14, issue.9, pp.801-805, 2004.
DOI : 10.1016/j.cub.2004.04.037

J. C. Carrington, Genome-Wide Profiling and Analysis of Arabidopsis siRNAs, PLOS Biology, vol.5, p.57, 2007.

J. Jin and H. , A pathogen-inducible endogenous siRNA in plant immunity, Proceedings of the National Academy of Sciences, vol.103, p.18002, 2006.

S. Kim and S. B. Gelvin, Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions, The Plant Journal, vol.94, issue.5, pp.779-791, 2007.
DOI : 10.1074/jbc.272.10.6799

V. N. Kim, J. Han, and M. C. Siomi, Biogenesis of small RNAs in animals, Nature Reviews Molecular Cell Biology, vol.274, issue.2, pp.126-139, 2009.
DOI : 10.4161/rna.1.1.943

Y. Kim, K. Schumacher, and J. K. Zhu, EMS mutagenesis of Arabidopsis, Methods in Molecular Biology, vol.323, pp.101-103, 2006.

H. Kwak and J. T. Lis, Control of Transcriptional Elongation, Annual Review of Genetics, vol.47, issue.1, pp.483-508, 2013.
DOI : 10.1146/annurev-genet-110711-155440

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974797/pdf

E. Lanet, E. Delannoy, R. Sormani, M. Floris, P. Brodersen et al., Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs, THE PLANT CELL ONLINE, vol.21, issue.6, pp.1762-1768, 2009.
DOI : 10.1105/tpc.108.063412

URL : https://hal.archives-ouvertes.fr/hal-00423302

J. A. Law and S. E. Jacobsen, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nature Reviews Genetics, vol.28, issue.3, pp.204-220, 2010.
DOI : 10.4161/epi.8974

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3034103/pdf

J. A. Law, A. A. Vashisht, J. A. Wohlschlegel, and S. E. Jacobsen, SHH1, a Homeodomain Protein Required for DNA Methylation, As Well As RDR2, RDM4, and Chromatin Remodeling Factors, Associate with RNA Polymerase IV, PLoS Genetics, vol.40, issue.7, p.1002195, 2011.
DOI : 10.1371/journal.pgen.1002195.s003

L. Masson, I. Jauvion, V. Bouteiller, N. Rivard, M. Elmayan et al., Mutations in the Arabidopsis H3K4me2/3 Demethylase JMJ14 Suppress Posttranscriptional Gene Silencing by Decreasing Transgene Transcription, The Plant Cell, vol.24, issue.9, pp.3603-3612, 2012.
DOI : 10.1105/tpc.112.103119

URL : https://hal.archives-ouvertes.fr/hal-01004532

J. Li, Z. Yang, J. Liu, and X. Chen, Methylation Protects miRNAs and siRNAs from a 3???-End Uridylation Activity in Arabidopsis, Current Biology, vol.15, issue.16, pp.1501-1507, 2005.
DOI : 10.1016/j.cub.2005.07.029

S. Li, L. E. Vandivier, L. Gao, S. Y. Won, S. Li et al., reveals features and regulation of siRNA biogenesis, Genome Research, vol.25, issue.2, p.235, 2014.
DOI : 10.1101/gr.182238.114

W. Li, H. Liu, Z. J. Cheng, Y. H. Su, H. N. Han et al., DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling, PLoS Genetics, vol.3, issue.8, p.1002243, 2011.
DOI : 10.1371/journal.pgen.1002243.s010

URL : https://doi.org/10.1371/journal.pgen.1002243

X. Liu, D. A. Bushnell, and R. D. Kornberg, RNA polymerase II transcription: Structure and mechanism, BBA) -Gene Regulatory Mechanisms 1829, 2013.
DOI : 10.1016/j.bbagrm.2012.09.003

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244541/pdf

F. Lu, X. Cui, S. Zhang, C. Liu, and X. Cao, JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis, Cell Research, vol.20, issue.3, pp.387-390, 2010.
DOI : 10.1016/j.cell.2008.08.036

URL : http://www.nature.com/cr/journal/v20/n3/pdf/cr201027a.pdf

I. J. Macrae, Structural Basis for Double-Stranded RNA Processing by Dicer, Science, vol.311, issue.5758, pp.195-198, 2006.
DOI : 10.1126/science.1121638

P. V. Maillard, C. Ciaudo, A. Marchais, Y. Li, F. Jay et al., Antiviral RNA Interference in Mammalian Cells, Science, vol.6, issue.15, pp.235-238, 2013.
DOI : 10.1186/1748-7188-6-26

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853215/pdf

A. Mallory and H. Vaucheret, Form, Function, and Regulation of ARGONAUTE Proteins, The Plant Cell, vol.22, issue.12, 2010.
DOI : 10.1105/tpc.110.080671

URL : https://hal.archives-ouvertes.fr/hal-01203875

A. C. Mallory and H. Vaucheret, ARGONAUTE 1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways, EMBO reports, vol.10, issue.5, pp.521-526, 2009.
DOI : 10.1073/pnas.0506426102

S. S. Mandal, C. Chu, T. Wada, H. Handa, A. J. Shatkin et al., Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II, Proceedings of the National Academy of Sciences, pp.7572-7577, 2004.
DOI : 10.1126/science.1085712

A. E. Martinez-de-alba, E. Elvira-matelot, and H. Vaucheret, Gene silencing in plants: A diversity of pathways, BBA) -Gene Regulatory Mechanisms 1829, pp.1300-1308, 2013.
DOI : 10.1016/j.bbagrm.2013.10.005

S. Balzergue, S. Aubourg, D. Gautheret, M. D. Crespi, H. Vaucheret et al., In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs, Nucleic Acids Research, vol.43, pp.2902-2913, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01204176

A. Marí-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.1029-1040, 2013.
DOI : 10.1093/bioinformatics/btq033

M. A. Matzke and R. A. 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

N. Maunoury and H. Vaucheret, AGO1 and AGO2 Act Redundantly in miR408-Mediated Plantacyanin Regulation, PLoS ONE, vol.81, issue.12, p.28729, 2011.
DOI : 10.1371/journal.pone.0028729.t001

URL : https://doi.org/10.1371/journal.pone.0028729

A. D. Mccue, S. Nuthikattu, S. H. Reeder, and R. K. 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. D. Mccue, K. Panda, S. Nuthikattu, S. G. Choudury, E. N. 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

S. Melquist and J. Bender, An Internal Rearrangement in an Arabidopsis Inverted Repeat Locus Impairs DNA Methylation Triggered by the Locus, Genetics, vol.166, issue.1, pp.437-448, 2004.
DOI : 10.1534/genetics.166.1.437

M. F. Mette, W. Aufsatz, J. Van-der-winden, M. A. Matzke, and A. J. Matzke, Transcriptional silencing and promoter methylation triggered by double-stranded RNA, The EMBO Journal, vol.101, issue.19, pp.5194-5201, 2000.
DOI : 10.1093/emboj/19.19.5194

URL : http://emboj.embopress.org/content/embojnl/19/19/5194.full.pdf

S. Mlotshwa, G. J. Pruss, Z. Gao, N. L. Mgutshini, J. Li et al., Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing, The Plant Journal, vol.299, issue.4, pp.699-704, 2010.
DOI : 10.1016/j.bbaexp.2003.10.015

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04358.x/pdf

V. Vance, RNA silencing and the mobile silencing signal. The Plant cell, 2002.

P. Dunoyer, A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing, Nucleic Acids Research, p.1264, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01546918

T. A. Montgomery, M. D. Howell, J. T. Cuperus, D. Li, J. E. Hansen et al., Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation, Cell, vol.133, issue.1, pp.128-141, 2008.
DOI : 10.1016/j.cell.2008.02.033

A. C. Mallory, Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants, Nucleic Acids Research, vol.41, pp.4699-4708, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01001529

J. Murfett, X. J. Wang, G. Hagen, and T. J. Guilfoyle, Identification of Arabidopsis Histone Deacetylase HDA6 Mutants That Affect Transgene Expression, THE PLANT CELL ONLINE, vol.13, issue.5, pp.1047-1061, 2001.
DOI : 10.1105/tpc.13.5.1047

H. Nagano, A. Fukudome, A. Hiraguri, H. Moriyama, and T. Fukuhara, Distinct substrate specificities of Arabidopsis DCL3 and DCL4, Nucleic Acids Research, vol.42, issue.3, pp.1845-1856, 2013.
DOI : 10.1093/nar/gkt1077

URL : https://academic.oup.com/nar/article-pdf/42/3/1845/17065537/gkt1077.pdf

C. Napoli, C. Lemieux, and R. Jorgensen, Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans, THE PLANT CELL ONLINE, vol.2, issue.4, pp.279-289, 1990.
DOI : 10.1105/tpc.2.4.279

U. Naumann, L. Daxinger, T. Kanno, C. Eun, Q. Long et al., Genetic Evidence That DNA Methyltransferase DRM2 Has a Direct Catalytic Role in RNA-Directed DNA Methylation in Arabidopsis thaliana, Genetics, vol.187, issue.3, pp.977-979, 2011.
DOI : 10.1534/genetics.110.125401

H. H. Ng, F. Robert, R. A. Young, and K. Struhl, Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity, Molecular Cell, vol.11, issue.3, pp.709-719, 2003.
DOI : 10.1016/S1097-2765(03)00092-3

E. Savitsky, P. Gileadi, O. Delft, V. , F. Rose et al., Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity, Nature, vol.448, pp.87-92, 2007.

S. Nuthikattu, A. D. Mccue, K. Panda, D. Fultz, C. Defraia et al., 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.2368-2379, 2013.
DOI : 10.1104/pp.113.216481

D. J. Obbard, K. H. Gordon, A. H. Buck, and F. M. Jiggins, The evolution of RNAi as a defence against viruses and transposable elements, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.20, issue.23, pp.99-115, 2008.
DOI : 10.1101/gad.1495506

A. N. Olsen, H. A. Ernst, . Leggio, L. Lo, and K. Skriver, NAC transcription factors: structurally distinct, functionally diverse, Trends in Plant Science, vol.10, issue.2, pp.79-86, 2005.
DOI : 10.1016/j.tplants.2004.12.010

J. C. Palauqui, T. Elmayan, and J. M. Pollien, Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions, The EMBO Journal, vol.16, issue.15, pp.4738-4745, 1997.
DOI : 10.1093/emboj/16.15.4738

URL : http://emboj.embopress.org/content/embojnl/16/15/4738.full.pdf

J. C. Palauqui, T. Elmayan, F. D. De-borne, P. Crete, C. Charles et al., Frequencies, Timing, and Spatial Patterns of Co-Suppression of Nitrate Reductase and Nitrite Reductase in Transgenic Tobacco Plants, Plant Physiology, vol.112, issue.4, pp.1447-1456, 1996.
DOI : 10.1104/pp.112.4.1447

H. Pan, S. Liu, and D. Tang, HPR1, a component of the THO/TREX complex, plays an important role in disease resistance and senescence in Arabidopsis, The Plant Journal, vol.407, issue.5, pp.831-843, 2011.
DOI : 10.1038/35030160

J. Parent, N. Bouteiller, T. Elmayan, and H. Vaucheret, Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing, The Plant Journal, vol.19, issue.2, pp.223-232, 2015.
DOI : 10.1101/gad.1352605

URL : https://hal.archives-ouvertes.fr/hal-01204112

J. Parent, V. Jauvion, N. Bouché, C. Béclin, M. Hachet et al., Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes, Nucleic Acids Research, vol.43, issue.17, pp.8464-8475, 2015.
DOI : 10.1093/nar/gkv753

URL : https://academic.oup.com/nar/article-pdf/43/17/8464/17434885/gkv753.pdf

W. Park, J. Li, R. Song, J. Messing, and X. Chen, CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thaliana, Current Biology, vol.12, issue.17, p.1484, 2002.
DOI : 10.1016/S0960-9822(02)01017-5

O. Porrua and D. Libri, Transcription termination and the control of the transcriptome: why, where and how to stop, Nature Reviews Molecular Cell Biology, vol.166, issue.3, p.190, 2015.
DOI : 10.1016/j.cell.2009.02.043

URL : https://hal.archives-ouvertes.fr/hal-01132404

A. V. Probst, M. Fagard, F. Proux, P. Mourrain, S. Boutet et al., Arabidopsis Histone Deacetylase HDA6 Is Required for Maintenance of Transcriptional Gene Silencing and Determines Nuclear Organization of rDNA Repeats, THE PLANT CELL ONLINE, vol.16, issue.4, pp.1021-1034, 2004.
DOI : 10.1105/tpc.018754

N. Pumplin and O. Voinnet, RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence, Nature Reviews Microbiology, vol.454, issue.11, p.745, 2013.
DOI : 10.1016/j.celrep.2013.08.018

N. Pumplin, A. Sarazin, P. E. Jullien, N. G. Bologna, S. Oberlin et al., Isoforms, Which Encode Proteins of Alternative Localization and Function, The Plant Cell, vol.28, issue.11, pp.2786-2804, 2016.
DOI : 10.1105/tpc.16.00554

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5155348/pdf

S. Puranik, P. P. Sahu, P. S. Srivastava, and M. Prasad, NAC proteins: regulation and role in stress tolerance, Trends in Plant Science, vol.17, issue.6, pp.369-381, 2012.
DOI : 10.1016/j.tplants.2012.02.004

P. Raja, B. C. Sanville, R. C. Buchmann, and D. M. Bisaro, Viral Genome Methylation as an Epigenetic Defense against Geminiviruses, Journal of Virology, vol.82, issue.18, pp.8997-9008, 2008.
DOI : 10.1128/JVI.00719-08

R. Rajagopalan, H. Vaucheret, J. Trejo, and D. P. Bartel, A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana, Genes & Development, vol.20, issue.24, pp.3407-3425, 2006.
DOI : 10.1101/gad.1476406

B. J. Reinhart, E. G. Weinstein, M. W. Rhoades, B. Bartel, and D. P. Bartel, MicroRNAs in plants, Genes & Development, vol.16, issue.13, pp.1616-1626, 2002.
DOI : 10.1101/gad.1004402

G. Ren, M. Xie, S. Zhang, C. Vinovskis, X. Chen et al., Methylation protects microRNAs from an AGO1-associated activity that uridylates 5' RNA fragments generated by AGO1 cleavage, Proceedings of the National Academy of Sciences, vol.12, issue.17, pp.6365-6370, 2014.
DOI : 10.1016/S0960-9822(02)01017-5

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035956/pdf

M. Ron, M. A. Saez, L. E. Williams, J. C. Fletcher, and S. Mccormick, Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis, Genes & Development, vol.24, issue.10, p.1010, 2010.
DOI : 10.1101/gad.1882810

F. Roudier, I. Ahmed, C. Bérard, A. Sarazin, T. Mary-huard et al., Integrative epigenomic mapping defines four main chromatin states in Arabidopsis, The EMBO Journal, vol.39, issue.10, pp.1928-1938, 2011.
DOI : 10.1038/ng1929

URL : https://hal.archives-ouvertes.fr/hal-00999846

H. Santos-rosa, R. Schneider, A. J. Bannister, J. Sherriff, B. E. Bernstein et al., Active genes are tri-methylated at K4 of histone H3, Nature, vol.102, issue.6905, pp.407-411, 2002.
DOI : 10.1101/gad.190301

C. Schalk, V. Cognat, S. Graindorge, T. Vincent, O. Voinnet et al., Small RNAmediated repair of UV-induced DNA lesions by the DNA DAMAGE-BINDING PROTEIN 2 and ARGONAUTE 1, Proceedings of the National Academy of Sciences, pp.1-10, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01521842

M. Schmid and T. H. Jensen, Nuclear quality control of RNA polymerase II transcripts, Wiley Interdisciplinary Reviews: RNA, vol.16, issue.3, 2010.
DOI : 10.1371/journal.pbio.1000008

R. A. Martienssen, Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana, PLoS ONE, vol.4, p.5980, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00856245

S. Schütz and P. Sarnow, Interaction of viruses with the mammalian RNA interference pathway, Virology, vol.344, issue.1, pp.151-157, 2005.
DOI : 10.1016/j.virol.2005.09.034

I. R. Searle, O. Pontes, C. W. Melnyk, L. M. Smith, and D. C. Baulcombe, JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis, Genes & Development, vol.24, issue.10, pp.986-991, 2010.
DOI : 10.1101/gad.579910

J. Secombe, L. Li, L. Carlos, and R. N. Eisenman, The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth, Genes & Development, vol.21, issue.5, pp.537-551, 2007.
DOI : 10.1101/gad.1523007

H. Shaked, N. Avivi-ragolsky, and A. L. Avraham, Involvement of the Arabidopsis SWI2/SNF2 Chromatin Remodeling Gene Family in DNA Damage Response and Recombination, Genetics, vol.173, issue.2, pp.985-994, 2006.
DOI : 10.1534/genetics.105.051664

D. C. Baulcombe, An SNF2 Protein Associated with Nuclear RNA Silencing and the Spread of a Silencing Signal between Cells in Arabidopsis, The Plant cell, vol.19, pp.1507-1521, 2007.

F. F. Souret, J. P. Kastenmayer, and P. J. Green, AtXRN4 Degrades mRNA in Arabidopsis and Its Substrates Include Selected miRNA Targets, Molecular Cell, vol.15, issue.2, pp.173-183, 2004.
DOI : 10.1016/j.molcel.2004.06.006

URL : https://doi.org/10.1016/j.molcel.2004.06.006

H. Stroud, T. Do, J. Du, X. Zhong, S. Feng et al., Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis, Nature Structural & Molecular Biology, vol.733, issue.1, p.64, 2013.
DOI : 10.1126/science.1221472

H. Stroud, M. V. Greenberg, S. Feng, Y. V. Bernatavichute, and S. E. Jacobsen, Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome, Cell, vol.152, issue.1-2, pp.352-364, 2013.
DOI : 10.1016/j.cell.2012.10.054

J. H. Tuteja, G. Zabala, K. Varala, M. Hudson, and L. O. Vodkin, Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family in Glycine max Seed Coats, The Plant Cell, vol.21, issue.10, pp.3063-3077, 2009.
DOI : 10.1105/tpc.109.069856

J. M. Vargason, G. Szittya, and J. Burgyán, Size Selective Recognition of siRNA by an RNA Silencing Suppressor, Cell, vol.115, issue.7, pp.799-811, 2003.
DOI : 10.1016/S0092-8674(03)00984-X

H. Vaucheret, Plant ARGONAUTES, Trends in Plant Science, vol.13, issue.7, pp.350-358, 2008.
DOI : 10.1016/j.tplants.2008.04.007

F. Vazquez, H. Vaucheret, R. Rajagopalan, C. Lepers, V. Gasciolli et al., Endogenous trans-Acting siRNAs Regulate the Accumulation of Arabidopsis mRNAs, Molecular Cell, vol.16, issue.1, pp.69-79, 2004.
DOI : 10.1016/j.molcel.2004.09.028

D. Vedova, C. B. Lorbiecke, R. Kirsch, H. Schulte, M. B. Scheets et al., The Dominant Inhibitory, J. A, 2005.

E. Verdin and M. Ott, 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond, Nature Reviews Molecular Cell Biology, vol.18, issue.4, pp.258-264, 2014.
DOI : 10.1128/MCB.01245-07

O. Voinnet, P. Vain, S. Angell, and D. C. Baulcombe, Systemic Spread of, 1998.

E. J. Wagner and P. B. Carpenter, Understanding the language of Lys36 methylation at histone H3, Nature Reviews Molecular Cell Biology, vol.282, issue.2, pp.115-126, 2012.
DOI : 10.1074/jbc.M607909200

X. B. Wang, Q. Wu, T. Ito, F. Cillo, W. X. Li et al., RNAimediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana, Proceedings of the National Academy of Sciences, pp.484-489, 2009.

P. M. Waterhouse, M. W. Graham, and M. B. Wang, Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA, Proceedings of the National Academy of Sciences, vol.391, issue.6669, pp.13959-13964, 1998.
DOI : 10.1038/35888

&. Qi and Y. , A Role for Small RNAs in DNA Double-Strand Break Repair, Cell, vol.149, pp.101-112, 2012.

A. T. Wierzbicki, T. S. Ream, J. R. Haag, and C. S. Pikaard, RNA polymerase V transcription guides ARGONAUTE4 to chromatin, Nature Genetics, vol.41, issue.5, pp.630-634, 2009.
DOI : 10.1016/S1097-2765(03)00477-5

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674513/pdf

J. Xiao, U. Lee, and D. Wagner, Tug of war: adding and removing histone lysine methylation in Arabidopsis, Current Opinion in Plant Biology, vol.34, pp.41-53, 2016.
DOI : 10.1016/j.pbi.2016.08.002

M. Xie, G. Ren, P. Costa-nunes, O. Pontes, and B. Yu, A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation, Nucleic Acids Research, vol.40, issue.10, pp.4422-4431, 2012.
DOI : 10.1093/nar/gks034

Z. Xie, L. K. Johansen, A. M. Gustafson, K. D. Kasschau, A. D. Lellis et al., Genetic and Functional Diversification of Small RNA Pathways in Plants, PLoS Biology, vol.299, issue.5, pp.642-652, 2004.
DOI : 10.1371/journal.pbio.0020104.sd002

J. Xu, J. Y. Yang, Q. W. Niu, and N. H. Chua, Arabidopsis DCP2, DCP1, and VARICOSE Form a Decapping Complex Required for Postembryonic Development, THE PLANT CELL ONLINE, vol.18, issue.12, pp.3386-3398, 2006.
DOI : 10.1105/tpc.106.047605

URL : http://www.plantcell.org/content/plantcell/18/12/3386.full.pdf

D. Yang, G. Zhang, K. Tang, J. Li, L. Yang et al., Dicer-independent RNA-directed DNA methylation in Arabidopsis, Cell Research, vol.26, issue.1, pp.66-82, 2015.
DOI : 10.1093/bioinformatics/btq033

URL : http://www.nature.com/cr/journal/v26/n11/pdf/cr2016122a.pdf

W. Yang, D. Jiang, J. Jiang, and Y. He, A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis, The Plant Journal, vol.8, issue.4, pp.663-673, 2010.
DOI : 10.1016/j.tplants.2005.01.008

Z. Yang, Y. W. Ebright, B. Yu, and X. Chen, HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide, Nucleic Acids Research, vol.34, issue.2, pp.667-675, 2006.
DOI : 10.1093/nar/gkj474

P. Arabidopsis and T. , TREX mRNA export complex is involved in transgene and endogenous siRNA biosynthesis, Proceedings of the National Academy of Sciences, vol.107, pp.13948-13953

J. Paszkowski, MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing, The EMBO journal, vol.29, p.340, 2009.

B. C. Yoo, A Systemic Small RNA Signaling System in Plants, THE PLANT CELL ONLINE, vol.16, issue.8, pp.1979-2000, 2004.
DOI : 10.1105/tpc.104.023614

URL : http://www.plantcell.org/content/plantcell/16/8/1979.full.pdf

M. Yoshikawa, A. Peragine, M. Y. Park, and R. S. Poethig, A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis, Genes & Development, vol.19, issue.18, pp.2164-2175, 2005.
DOI : 10.1101/gad.1352605

A. Yu, B. Saudemont, N. Bouteiller, E. Elvira-matelot, G. Lepère et al., as an Endogenous Suppressor of Transgene Posttranscriptional Gene Silencing, Plant Physiology, vol.169, issue.2, pp.1266-1274, 2015.
DOI : 10.1104/pp.15.00585

L. Zilberman and D. , The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin, Cell, vol.153, pp.193-205, 2013.

J. Bartolome, W. Liu, I. R. Henderson, B. C. Meyers, I. Ausin et al., A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis, Cell, vol.163, pp.445-455, 2015.

C. Zhang, Z. Wu, Y. Li, and J. Wu, Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants, Frontiers in Microbiology, vol.447, issue.e46238, pp.1-12, 2015.
DOI : 10.1016/j.gene.2009.07.004

S. Zhang, B. Zhou, Y. Kang, X. Cui, A. Liu et al., C-terminal domains of histone demethylase JMJ14 interact with a pair of NAC transcription factors to mediate specific chromatin association, Cell Discovery, vol.6, pp.1-13, 2015.
DOI : 10.1093/nar/30.1.207

X. Zhang, Y. R. Yuan, Y. Pei, S. S. Lin, T. Tuschl et al., Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense, Genes & Development, vol.20, issue.23, pp.3255-3268, 2006.
DOI : 10.1101/gad.1495506

URL : http://genesdev.cshlp.org/content/20/23/3255.full.pdf

X. Zhang, H. Zhao, S. Gao, W. Wang, S. Katiyar-agarwal et al., Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393???-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12, Molecular Cell, vol.42, issue.3, pp.12-356, 2011.
DOI : 10.1016/j.molcel.2011.04.010

X. Zhang, Y. Zhu, H. Wu, and H. Guo, Post-transcriptional gene silencing in plants: a double-edged sword, Science China Life Sciences, vol.348, issue.3, pp.271-276, 2015.
DOI : 10.1126/science.aaa2618

Z. Zhang, X. Liu, X. Guo, X. Wang, and X. Zhang, Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing, Nature Plants, vol.2, issue.5, p.16049, 2016.
DOI : 10.7554/eLife.06671

X. Zheng, J. Zhu, A. Kapoor, and J. Zhu, Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing, The EMBO Journal, vol.14, issue.6, pp.1691-1701, 2007.
DOI : 10.1038/sj.emboj.7601603

X. Zhong, J. Du, C. J. Hale, J. Gallego-bartolome, S. Feng et al., Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases, Cell, vol.157, issue.5, pp.1050-1060, 2014.
DOI : 10.1016/j.cell.2014.03.056

H. Zhu, F. Hu, R. Wang, X. Zhou, S. Sze et al., Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development, Cell, vol.145, issue.2, pp.242-256, 2011.
DOI : 10.1016/j.cell.2011.03.024

URL : https://doi.org/10.1016/j.cell.2011.03.024

P. A. Ziolkowski, C. J. Underwood, C. Lambing, M. Martinez-garcia, E. J. Lawrence et al., crossover recombination, Genes & Development, vol.3, issue.3, pp.306-317, 2017.
DOI : 10.7554/eLife.03708

F. De-carvalho, G. Gheysen, S. Kushnir, M. Van-montagu, D. Inze et al., Suppression of beta-1, 3-glucanase transgene expression in homozygous plants, The EMBO journal, vol.11, pp.2595-2602, 1992.

R. P. Van-rij and E. Berezikov, Small RNAs and the control of transposons and viruses in Drosophila, Trends in Microbiology, vol.17, issue.4, pp.163-171, 2009.
DOI : 10.1016/j.tim.2009.01.003