Heterochromatin revisited, Nat Rev Genet, vol.8, issue.1, pp.35-46, 2007. ,
Transposable elements and the epigenetic regulation of the genome, Nat Rev Genet, vol.8, issue.4, pp.272-85, 2007. ,
Regulation of transposable elements by DNA modifications, Nat Rev Genet, vol.20, issue.7, p.30867571, 2019. ,
How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes, Trends Genet, vol.35, issue.6, pp.457-69, 2019. ,
Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat Rev Genet, vol.11, issue.3, pp.204-224, 2010. ,
RNA-directed DNA methylation: an epigenetic pathway of increasing complexity, Nat Rev Genet, vol.15, issue.6, pp.394-408, 2014. ,
The RNAs of RNA-directed DNA methylation, Biochim Biophys Acta, 2016. ,
DNA methylation pathways and their crosstalk with histone methylation, Nat Rev Mol Cell Biol, vol.16, issue.9, pp.519-551, 2015. ,
Dynamics and function of DNA methylation in plants, Nat Rev Mol Cell Biol, vol.19, issue.8, p.29784956, 2018. ,
The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin, Cell, vol.153, issue.1, pp.193-205, 2013. ,
Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis, Nat Struct Mol Biol, vol.21, issue.1, pp.64-72, 2014. ,
MORC family ATPases required for heterochromatin condensation and gene silencing, Science, vol.336, issue.6087, pp.1448-51, 2012. ,
Transcriptional gene silencing by Arabidopsis microrchidia homologues involves the formation of heteromers, Proc Natl Acad Sci U S A, vol.111, issue.20, pp.7474-7483, 2014. ,
Involvement of a GHKL ATPase in RNA-directed DNA methylation in Arabidopsis thaliana, Curr Biol, vol.22, issue.10, pp.933-941, 2012. ,
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
Identification of MAIN, a factor involved in genome stability in the meristems of Arabidopsis thaliana, Plant J, vol.75, issue.3, pp.469-83, 2013. ,
MAIN-LIKE1 is a crucial factor for correct cell division and differentiation in Arabidopsis thaliana, Plant J, vol.78, issue.1, pp.107-127, 2014. ,
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons, Nucleic Acids Res, vol.34, issue.22, pp.6505-6525, 2006. ,
A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons, Genetica, vol.139, issue.11-12, p.22544262, 2011. ,
Arabidopsis PPP family of serine/threonine phosphatases, Trends Plant Sci, vol.12, issue.4, pp.169-76, 2007. ,
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, issue.5, p.1002674, 2012. ,
Calmodulin-binding protein phosphatase PP7 is involved in thermotolerance in Arabidopsis, Plant Cell Environ, vol.30, issue.2, p.17238907, 2007. ,
The protein phosphatase 7 regulates phytochrome signaling in Arabidopsis, PLoS One, vol.3, issue.7, p.2699, 2008. ,
Arabidopsis PPP family of serine/threonine protein phosphatases: many targets but few engines, Trends Plant Sci, vol.18, issue.9, pp.505-518, 2013. ,
Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance, Plant Physiol, 2019. ,
Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome, Cell, vol.152, issue.1-2, pp.352-64, 2013. ,
From nucleosome to chromosome: a dynamic organization of genetic information, Plant J, vol.66, issue.1, p.21443619, 2011. ,
Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation, Cell Res, vol.29, issue.1, p.30425322, 2019. ,
Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis, Plant J, vol.50, issue.5, p.17470059, 2007. ,
MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing, Embo J, vol.29, issue.2, pp.340-51 ,
mille-feuille" of silencing: epigenetic control of transposable elements, Biochim Biophys Acta, vol.1809, issue.8, pp.452-460, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01917175
Who's your neighbor? New computational approaches for functional genomics, Nat Biotechnol, vol.18, issue.6, pp.609-622, 2000. ,
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana, Plant J, vol.16, issue.6, pp.735-778, 1998. ,
HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing, Plant Physiol, vol.168, issue.4, pp.1298-308, 2015. ,
Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, vol.30, pp.2114-2134, 2014. ,
HISAT: a fast spliced aligner with low memory requirements, Nat Methods, vol.12, issue.4, pp.357-60, 2015. ,
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009. ,
HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, issue.2, pp.166-175, 2015. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, issue.12, p.25516281, 2014. ,
limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, vol.43, issue.7, 2015. ,
Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis, Plant Physiol, vol.139, issue.1, pp.5-17, 2005. ,
SUITE: tools for motif discovery and searching, Nucleic Acids Res, vol.37, pp.202-210, 2009. ,
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, vol.27, issue.11, pp.1571-1573, 2011. ,
ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data, Bioinformatics, vol.34, issue.4, pp.708-717, 2018. ,
DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts, Nucleic Acids Res, vol.46, p.114, 2018. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, issue.5, pp.1792-1799, 2004. ,