DNA METHYLTRANSFERASE 3 (MET3) IS REGULATED BY POLYCOMB GROUP COMPLEX DURING ARABIDOPSIS ENDOSPERM DEVELOPMENT
METHYLOME DYNAMICS UPON PROTEASOME INHIBITION BY THE PSEUDOMONAS VIRULENCE FACTOR SYRINGOLIN A
DNA methylation is an important epigenetic mark required for proper gene expression and silencing of transposable elements. DNA methylation patterns can be modified by environmental factors such as pathogen infection, where modification of DNA methylation can be associated with plant resistance. To counter the plant defense pathways, pathogens produce effectors molecule, several of which act as proteasome inhibitors. Here we investigated the effect of proteasome inhibition by the bacterial virulence factor Syringolin A on genome-wide DNA methylation. We show that Syringolin A treatment results in an increase of DNA methylation at centromeric and pericentromeric regions of Arabidopsis chromosomes. We identify several CHH DMRs that are enriched in the proximity of transcriptional start sites. Syringolin A treatment does not result in significant changes in small RNA composition. However, significant changes in genome transcriptional activity can be observed, including a strong upregulation of resistance genes that are located on chromosomal arms. We hypothesize that DNA methylation changes could be linked to the upregulation of some atypical members of the de novo DNA methylation pathway: AGO3, AGO9 and DRM1. Our data suggests that modification of genome-wide DNA methylation resulting from an inhibition of the proteasome by bacterial effectors could be part of a epi-genomic arms race against pathogens.
Complex epigenetic changes occur during plant reproduction. These regulations ensure the proper transmission of epigenetic information as well as allowing for zygotic totipotency. In Arabidopsis, the main DNA methyltransferase is called MET1 and is responsible for methylating cytosine in the CG context. The Arabidopsis genome encodes for three additional reproduction-specific homologs of MET1, namely MET2a, MET2b and MET3. In this paper, we show that the DNA methyltransferase MET3 is expressed in the seed endosperm and its expression is further restricted to the chalazal endosperm. MET3 is biallelically expressed in the endosperm but displays a paternal expression bias. We found that MET3 expression is regulated by the Polycomb complex proteins FIE and MSI1. Seed development is not impaired in met3 mutant, and we could not observe significant transcriptional changes in met3 mutant. Interestingly, we found that MET3 regulates gene expression in a Polycomb mutant background suggesting a further complexification of the interplay between H3K27me3 and DNA methylation in the seed endosperm.
Tirot L, and Jullien PE*.DNA METHYLTRANSFERASE 3 (MET3) is regulated by Polycomb Group complex during Arabidopsis endosperm development. bioRxiv. https://doi.org/10.1101/2021.06.28.450243
Bonnet DMV, Grob S, Tirot L and Jullien PE*. Methylome dynamics upon proteasome inhibition by the pseudomonas virulence factor Syringolin A. BioXriv. https://doi.org/10.1101/2021.01.19.
Devers, Emanuel A.; Brosnan, Christopher A.; Sarazin, Alexis; Albertini, Daniele; Amsler, Andrea C.; Brioudes, Florian; Jullien, Pauline E.; Lim, Peiqi; Schott, Gregory; Voinnet, Olivier (2020). Movement and differential consumption of short interfering RNA duplexes underlie mobile RNA interference. Nature plants, 6(7), pp. 789-799. Springer Nature 10.1038/s41477-020-0687-2
Jullien, P.E., Grob, S., Marchais, A., Pumplin, N., Chevalier, C., Bonnet, D.M., Otto, C., Schott, G. and Voinnet, O. (2020), Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissues. Plant J. Accepted Author Manuscript. doi:10.1111/tpj.14868
Jullien, pauline E., Bonnet, D.M. V, Pumplin, N., Schroeder, J.A. and Voinnet, O. (2020) ASYMMETRIC EXPRESSION OF ARGONAUTES IN ARABIDOPSIS REPRODUCTIVE TISSUES. bioRxiv, 2020.05.18.102863. Available at: http://biorxiv.org/content/early/2020/05/19/2020.05.18.102863.abstract.
2018 and older
Jullien, Pauline E.; Grob, Stefan; Marchais, Antonin; Pumplin, Nathan; Chevalier, Clement; Otto, Caroline; Schott, Gregory; Voinnet, Olivier (18 December 2018). Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissue (bioRxiv 500769). Cold Spring Harbor Laboratory 10.1101/500769
Tschopp, MA; Iki; T, Brosnan, CA; Jullien, PE; Pumplin, N. (2017). A complex of Arabidopsis DRB proteins can impair dsRNA processing. RNA, 23, pp. 782-797. 10.1261/rna.059519.116
Pumplin, N; Sarazin, A; Jullien, PE; Bologna, NG; Oberlin, S; Voinnet, O. (2016). DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function. The Plant Cell, 28(11), pp. 2786-2804. 10.1105/tpc.16.00554
Calarco, JP; Borges, F; Donoghue, MT; van Ex, F; Jullien, PE; Lopes, T; Gardner, R; Berger, F; Feijó, JA; Becker, JD; Martienssen, RA. (2012). Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell, 151(1), pp. 194-205. 10.1016/j.cell.2012.09.001
Jullien, PE; Susaki, D; Yelagandula, R; Higashiyama, T; Berger, F. (2012). DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana. Current Biology, 22(19), pp. 1825-1830. 10.1016/j.cub.2012.07.061
Jullien, PE; Berger, F. (2010). DNA methylation reprogramming during plant sexual reproduction? Trends in Genetics, 26(9), pp. 394-399. 10.1016/j.tig.2010.06.001
Jullien, PE; Berger, F. (2010). Parental Genome Dosage Imbalance Deregulates Imprinting in Arabidopsis. PLoS Genetics, 6(3), e1000885. 10.1371/journal.pgen.1000885
Jullien, PE; Berger, F. (2009). Gamete-specific epigenetic mechanisms shape genomic imprinting. Current Opinion in Plant Biology 12(5), pp. 637-642. 10.1016/j.pbi.2009.07.004
Jullien, PE; Berger, F. (2008). Parental genomic imprinting in plants: significance for reproduction. Medecine sciences, 24(8-9), pp. 753-757. 10.1051/medsci/20082489753
Jullien, PE; Mosquna, A; Ingouff, M; Sakata, T; Ohad, N; Berger, F. (2008). Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biology, 6(8), e194. 10.1371/journal.pbio.0060194
Aubourg, S; Martin-Magniette, ML; Brunaud, V; Taconnat, L; Bitton, F; Balzergue, S; Jullien, PE; Ingouff, M; Thareau, V; Schiex, T; Lecharny, A; Renou, JP. (2007). Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. BMC Genomics, 8, 401. 10.1186/1471-2164-8-401
Ingouff, M; Jullien, PE; Berger, F. (2006). The female gametophyte and the endosperm control cell proliferation and differentiation of the seed coat in Arabidopsis. The Plant Cell, 18(12), pp. 3491-3501. 10.1105/tpc.106.047266
Jullien, PE; Kinoshita, T; Ohad, N; Berger, F. (2006). Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. The Plant Cell, 18(6), pp. 1360-1372. 10.1105/tpc.106.041178
Jullien, PE; Katz, A; Oliva, M; Ohad, N; Berger, F. (2006) Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Current Biology, 16(5), pp. 486-492. 10.1016/j.cub.2006.01.020