title: An Arabidopsis Natural Epiallele Maintained by a Feed-Forward Silencing Loop between Histone and DNA.
abstract: The extent of epigenetic variation is currently well documented, but the number of natural epialleles described so far remains very limited. Determining the relevance of epigenetic changes for natural variation is an important question of research that we investigate by isolating natural epialleles segregating in Arabidopsis recombinant populations. We previously described a genetic incompatibility among Arabidopsis strains based on the silencing of a gene involved in fitness. Here, we isolated a new epiallele resulting from the silencing of a transfer-RNA editing gene in an Arabidopsis accession from the Netherlands (Nok-1). Crosses with the reference accession Col-0 show a complete incompatibility between this epiallele and another locus localized on a different chromosome. We demonstrate that conversion of an unmethylated version of this allele occurs in hybrids, associated with modifications of small RNA populations. These epialleles can also spontaneously revert within the population. Furthermore, we bring evidence that neither METHYLTRANSFERASE 1, maintaining methylation at CGs, nor components of RNA-directed DNA methylation, are key factors for the transmission of the epiallele over generations. This depends only on the self-reinforcing loop between CHROMOMETHYLASE 3 and KRYPTONITE, involving DNA methylated in the CHG context and histone H3 lysine 9 methylation. Our findings reveal a predominant role of this loop in maintaining a natural epiallele.
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Astrid
authors.initials: A
authors.lastname: Agorio
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Durand
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Elisa
authors.identifier: 0000-0001-6788-0231
authors.initials: E
authors.lastname: Fiume
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Brousse
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Gy
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Simon
authors.affiliation: Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Sarit
authors.initials: S
authors.lastname: Anava
authors.affiliation: Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Oded
authors.initials: O
authors.lastname: Rechavi
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Loudet
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Camilleri
authors.affiliation: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Nicolas
authors.identifier: 0000-0002-3800-2613
authors.initials: N
authors.lastname: Bouché
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics; D044127:Epigenesis, Genetic; D025461:Feedback, Physiological; D020868:Gene Silencing; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D008780:Methyltransferases / Q000235:genetics / Q000378:metabolism; D011499:Protein Processing, Post-Translational
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D006657:Histones; D008780:Methyltransferases