Dynamic Chromatin State Profiling Reveals Regulatory Principle of Pluripotency During Shoot Regeneration

Genome-editing technologies have advanced in recent years but designing future crops is still limited by current methods of improving shoot regenerative capacity. Shoot regeneration is mediated by the sequential action of two phytohormones, auxin and cytokinin. However, the chromatin regulatory landscapes underlying this dynamic response have not yet been studied. In this study, we jointly profiled chromatin accessibility, histone modifications, and transcriptomes to demonstrate that a high-auxin environment primes shoot regeneration by increasing the accessibility of the gene loci associated with pluripotency and shoot fate determination. Cytokinin signaling not only triggers the commitment of the shoot progenitor at later stages, but allows chromatin to maintain shoot identity genes at the priming stage. Our analysis of transcriptional regulatory dynamics further identifies a catalog of regeneration cis-elements dedicated to cell fate transitions, and uncovers previously unrecognized roles of BES1, MYC, IDD, and PIF transcription factors in shoot regeneration. Our results provide a comprehensive resource for studying somatic cell reprogramming in plants and provides potential targets for improving future shoot regeneration efficiency.