J. M. Alonso, A. N. Stepanova, and T. J. Leisse, Genome-wide insertional mutagenesis of Arabidopsis thaliana, Science, vol.301, pp.653-657, 2003.

S. Amiard, M. E. Gallego, C. I. White, A. Bleckmann, S. Weidtkamp-peters et al., Stem cell signaling in Arabidopsis requires CRN to localize CLV2 to the plasma membrane, Front. Plant Sci, vol.4, pp.166-176, 2010.

D. C. Boyes, A. M. Zayed, R. Ascenzi, A. J. Mccaskill, N. E. Hoffman et al., Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants, Plant Cell, vol.13, pp.1499-1510, 2001.

S. H. Choi, T. H. Ryu, J. I. Kim, S. Lee, S. S. Lee et al., Mutation in DDM1 inhibits the homology directed repair of double strand breaks, PLoS ONE One, vol.14, 2019.

S. J. Clough and A. F. Bent, Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana, Plant J, vol.16, pp.735-743, 1998.

K. M. Culligan, C. E. Robertson, J. Foreman, P. Doerner, and A. B. Britt, ATR and ATM play both distinct and additive roles in response to ionizing radiation, Plant J, vol.48, pp.947-961, 2006.

M. D. Curtis and U. Grossniklaus, A gateway cloning vector set for high-throughput functional analysis of genes in planta, Plant Physiol, vol.133, pp.462-469, 2003.

M. Diaz, P. Pecinkova, A. Nowicka, C. Baroux, T. Sakamoto et al., The SMC5/6 complex subunit NSE4A is involved in DNA damage repair and seed development, Plant Cell, vol.31, pp.1579-1597, 2019.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013.

G. Drechsel, J. Bergler, K. Wippel, N. Sauer, K. Vogelmann et al., C-terminal armadillo repeats are essential and sufficient for association of the plant U-box armadillo E3 ubiquitin ligase SAUL1 with the plasma membrane, J. Exp. Bot, vol.62, pp.775-785, 2011.

J. Du, L. M. Johnson, S. E. Jacobsen, and D. J. Patel, DNA methylation pathways and their crosstalk with histone methylation, Nat. Rev. Mol. Cell Biol, vol.16, pp.519-532, 2015.

I. Farkas, V. Dombradi, M. Miskei, L. Szabados, and C. Koncz, Arabidopsis PPP family of serine/threonine phosphatases, Trends Plant Sci, vol.12, pp.169-176, 2007.

W. Feng and S. D. Michaels, Accessing the inaccessible: the organization, transcription, replication, and repair of heterochromatin in plants, Annu. Rev. Genet, vol.49, pp.439-459, 2015.

P. F. Fransz and J. H. De-jong, Chromatin dynamics in plants, Curr. Opin. Plant Biol, vol.5, pp.560-567, 2002.

N. Fulcher and R. Sablowski, Hypersensitivity to DNA damage in plant stem cell niches, Proc. Natl Acad. Sci. USA, vol.106, pp.20984-20988, 2009.

T. Furukawa, M. J. Curtis, C. M. Tominey, Y. H. Duong, B. W. Wilcox et al., A shared DNA-damage-response pathway for induction of stem-cell death by UVB and by gamma irradiation, DNA Repair (Amst), vol.9, pp.940-948, 2010.

T. Genoud, M. T. Santa-cruz, T. Kulisic, F. Sparla, C. Fankhauser et al., The protein phosphatase 7 regulates phytochrome signaling in Arabidopsis, PLoS ONE One, vol.3, p.2699, 2008.

R. D. Gietz, B. Triggs-raine, A. Robbins, K. C. Graham, and R. A. Woods, Identification of proteins that interact with a protein of interest: applications of the yeast two-hybrid system, Mol. Cell Biochem, vol.172, pp.67-79, 1997.

C. Grefen and M. R. Blatt, A 2in1 cloning system enables ratiometric bimolecular fluorescence complementation (rBiFC), Biotechniques, vol.53, pp.311-314, 2012.

R. Heidstra and S. Sabatini, Plant and animal stem cells: similar yet different, Nat. Rev. Mol. Cell Biol, vol.15, pp.301-312, 2014.

J. Hellemans, G. Mortier, A. De-paepe, F. Speleman, and J. Vandesompele, ) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data, 2007.

, Genome Biol, vol.8, p.19

J. Heyman, T. Cools, and F. Vandenbussche, ERF115 controls root quiescent center cell division and stem cell replenishment, Science, vol.342, pp.860-863, 2013.

B. M. Horvath, H. Kourova, and S. Nagy, Arabidopsis RETINOBLAS-TOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control, EMBO J, vol.36, pp.1261-1278, 2017.

Z. Hu, T. Cools, and L. De-veylder, Mechanisms used by plants to cope with DNA damage, Annu. Rev. Plant Biol, vol.67, pp.439-462, 2016.

Y. Ikeda, T. Pelissier, P. Bourguet, C. Becker, M. N. Pouch-pelissier et al., Arabidopsis proteins with a transposon-related domain act in gene silencing, Nat. Commun, vol.8, p.15122, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01917158

N. Jia, X. Liu, and H. Gao, A DNA2 homolog is required for DNA damage repair, cell cycle regulation, and meristem maintenance in plants, Plant Physiol, vol.171, pp.318-333, 2016.

R. A. Johnson, P. A. Conklin, M. Tjahjadi, V. Missirian, T. Toal et al., SUPPRESSOR OF GAMMA RESPONSE1 links DNA damage response to organ regeneration, Plant Physiol, vol.176, pp.1665-1675, 2018.

S. Kosugi, M. Hasebe, M. Tomita, and H. Yanagawa, Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs, Proc. Natl Acad. Sci. USA, vol.106, pp.10171-10176, 2009.

Y. Kurihara, A. Matsui, and M. Kawashima, Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis, Biochem. Biophys. Res. Commun, vol.376, pp.553-557, 2008.

Y. Liao, G. K. Smyth, and W. Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, vol.30, pp.923-930, 2014.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

J. Ma, Y. Liu, W. Zhou, Y. Zhu, A. Dong et al., Histone chaperones play crucial roles in maintenance of stem cell niche during plant root development, Plant J, vol.95, pp.86-100, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01851865

G. Moissiard, S. J. Cokus, and J. Cary, MORC family ATPases required for heterochromatin condensation and gene silencing, Science, vol.336, pp.1448-1451, 2012.

S. G. Moller, Y. S. Kim, T. Kunkel, and N. H. Chua, PP7 is a positive regulator of blue light signaling in Arabidopsis, Plant Cell, vol.15, pp.1111-1119, 2003.

M. U. Nisa, Y. Huang, M. Benhamed, and C. Raynaud, The plant DNA damage response: signaling pathways leading to growth inhibition and putative role in response to stress conditions, Front. Plant Sci, vol.10, p.653, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02351967

J. Raya-gonzalez, A. Oropeza-aburto, J. S. Lopez-bucio, A. A. Guevara-garcia, L. De-veylder et al., MED-IATOR18 influences Arabidopsis root architecture, represses auxin signaling and is a critical factor for cell viability in root meristems, Plant J, vol.96, pp.895-909, 2018.

V. Reiterer, P. A. Eyers, and H. Farhan, Day of the dead: pseudokinases and pseudophosphatases in physiology and disease, Trends Cell Biol, vol.24, pp.489-505, 2014.

A. Sancar, L. A. Lindsey-boltz, K. Unsal-kacmaz, and S. Linn, Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints, Annu. Rev. Biochem, vol.73, pp.39-85, 2004.

C. A. Sjogren, S. C. Bolaris, and P. B. Larsen, Aluminum-dependent terminal differentiation of the Arabidopsis root tip is mediated through an ATR-, ALT2-, and SOG1-regulated transcriptional response, Plant Cell, vol.27, pp.2501-2515, 2015.

X. Sun, X. Kang, and M. Ni, Hypersensitive to red and blue 1 and its modification by protein phosphatase 7 are implicated in the control of Arabidopsis stomatal aperture, PLoS Genet, vol.8, 2012.

E. Truernit, H. Bauby, B. Dubreucq, O. Grandjean, J. Runions et al., High-resolution whole-mount imaging of three-dimensional tissue organization and gene expression enables the study of Phloem development and structure in Arabidopsis, Plant Cell, vol.20, pp.1494-1503, 2008.

S. Tsukahara, A. Kobayashi, A. Kawabe, O. Mathieu, A. Miura et al., Bursts of retrotransposition reproduced in Arabidopsis, Nature, vol.461, pp.423-426, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01917186

C. Uhlken, B. Horvath, R. Stadler, N. Sauer, and M. Weingartner, MAIN-LIKE1 is a crucial factor for correct cell division and differentiation in Arabidopsis thaliana, Plant J, vol.78, pp.107-120, 2014.

C. Uhlken, S. Hoth, and M. Weingartner, MAIL1 is essential for development of the primary root but not of anchor roots, Plant Signal Behav, vol.9, p.976477, 2014.

R. G. Uhrig, A. M. Labandera, and G. B. Moorhead, Arabidopsis PPP family of serine/threonine protein phosphatases: many targets but few engines, Trends Plant Sci, vol.18, pp.505-513, 2013.

J. Wang, T. Blevins, R. Podicheti, J. R. Haag, E. H. Tan et al., Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes, Genes Dev, vol.31, pp.1601-1614, 2017.

J. R. Wendrich, S. Boeren, B. K. Moller, D. Weijers, and B. De-rybel, In vivo identification of plant protein complexes using IP-MS/MS, Methods Mol. Biol, vol.1497, pp.147-158, 2017.

J. R. Wendrich, B. K. Moller, S. Li, S. Saiga, R. Sozzani et al., Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem, Proc. Natl Acad. Sci. USA, vol.114, pp.8922-8929, 2017.

U. Wenig, S. Meyer, R. Stadler, S. Fischer, D. Werner et al., Identification of MAIN, a factor involved in genome stability in the meristems of Arabidopsis thaliana, Plant J, vol.75, pp.469-483, 2013.

D. Xu, G. Marino, A. Klingl, B. Enderle, E. Monte et al., Extrachloroplastic PP7L functions in chloroplast development and abiotic stress tolerance, Plant Physiol, vol.180, pp.323-341, 2019.

D. Yi, C. L. Alvim-kamei, and T. Cools, The arabidopsis SIAMESE-RELATED cyclin-dependent kinase inhibitors SMR5 and SMR7 regulate the DNA damage checkpoint in response to reactive oxygen species, Plant Cell, vol.26, pp.296-309, 2014.

K. Yoshiyama, P. A. Conklin, N. D. Huefner, and A. B. Britt, Suppressor of gamma response 1 (SOG1) encodes a putative transcription factor governing multiple responses to DNA damage, Proc. Natl Acad. Sci. USA, vol.106, pp.12843-12848, 2009.

K. O. Yoshiyama, J. Kobayashi, N. Ogita, M. Ueda, S. Kimura et al., ATM-mediated phosphorylation of SOG1 is essential for the DNA damage response in Arabidopsis, EMBO Rep, vol.14, pp.817-822, 2013.

K. O. Yoshiyama, K. Kaminoyama, T. Sakamoto, and S. Kimura, Increased phosphorylation of Ser-Gln sites on SUPPRESSOR OF GAMMA RESPONSE1 strengthens the DNA damage response in Arabidopsis thaliana, Plant Cell, vol.29, pp.3255-3268, 2017.