Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression

The formation of symbiotic nodule cells in Medicago truncatula is driven by successive endoreduplication cycles and transcriptional reprogramming in different temporal waves including the activation of more than 600 cysteine-rich NCR genes expressed only in nodules. We show here that the transcriptional waves correlate with growing ploidy levels and have investigated how the epigenome changes during endoreduplication cycles. Differential DNA methylation was found in only a small subset of symbiotic nodule-specific genes, including more than half of the NCR genes, whereas in most genes DNA methylation was unaffected by the ploidy levels and was independent of the genes' active or repressed state. On the other hand, expression of nodule-specific genes correlated with ploidy-dependent opening of the chromatin as well as, in a subset of tested genes, with reduced H3K27me3 levels combined with enhanced H3K9ac levels. Our results suggest that endoreduplication-dependent epigenetic changes contribute to transcriptional reprogramming in the differentiation of symbiotic cells.

Citation

Nagymihály M, Veluchamy A, Györgypál Z, Ariel F, Jégu T, et al. (2017) Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression. Proceedings of the National Academy of Sciences 114: 4543–4548. Available: http://dx.doi.org/10.1073/pnas.1704211114.

Sponsors

We thank Célia Casset for help with the qPCR experiments, Dr. Mickael Bourge for the flow cytometry sorting of nodule nuclei, and Dr. István Nagy for providing the MBD2 protein for the MeDIP experiment. This work benefitted from the facilities and expertise of the Imagif Cell Biology Unit of the Gif campus (which is supported by the Infrastructures en Biologie Santé et Agronomie), the Agence Nationale de la Recherche (ANR) under Investments for the Future programs France-BioImaging Infrastructure Grant ANR-10-INSB-04-01 and Saclay Plant Sciences Grant ANR-10-LABX-0040-SPS, and the Conseil Général de l’Essonne. This work was supported by ANR Grant ANR-13-BSV7-0013 and by European Research Council SYM-BIOTICS Advanced Grant 269067 (to É.K.). M.N. was the recipient of a PhD grant from CAMPUS France and was supported by the SYM-BIOTICS grant.