The H3K27me3 epigenetic mark is crucial for callus cell identity and for the acquisition of new fate during root and shoot regeneration

Abstract

We combined molecular, genomic and genetic approaches to study the molecular mechanisms underlying cell totipotency and competency to regenerate in Arabidopsis. By performing comparative analysis of mRNA-seq and chromatin landscapes between leaf differentiated cells and callus totipotent cells and between WT callus and calli derived from the emf2 mutant, exhibiting impaired regenerative capacity we revealed the following: 1. That callus cells express numerous genes of many developmental pathways such as root, leaf, embryo, shoot, meristem and seed. This suggests a mechanism to allow rapid response to a signal by maintaining genes of all potential developmental pathways active, without the needs to release transcriptional silencing and to go through the intricate multistep process of transcription. 2. That key transcription factors that are sufficient to derive differentiation or organogenesis are silenced and marked by the H3K27me3. 3. That callus derived from the emf2 mutant which is impaired in setting the H3K27methylation, lost the capacity to regenerate and that 78 transcription factors from which 18 regulate flower development, where up-regulated compared with WT callus. Altogether our results suggest that competency to regenerate is achieved by keeping the chromatin of developmental genes active, and that upon a signal for cell fate switch, a mechanism to repress those genes is required to allow the one desired developmental pathway to dominate. When this mechanism is impaired the capacity to regenerate is decline.