DEMETER DNA demethylase reshapes the global DNA methylation landscape and controls cell identity transition during plant regeneration.

Background: Plants possess a high potential for somatic cell reprogramming, enabling the transition from differentiated tissue to pluripotent callus, followed by the formation of de novo shoots during plant regeneration. Despite extensive studies on the molecular network and key genetic factors involved in this process, the underlying epigenetic landscape remains incompletely understood.

Results: Here, we explored the dynamics of the methylome and transcriptome during the two-step plant regeneration process.

Callus proliferation-induced hypoxic microenvironment decreases shoot regeneration competence in Arabidopsis.

Plants are aerobic organisms that rely on molecular oxygen for respiratory energy production. Hypoxic conditions, with oxygen levels ranging between 1% and 5%, usually limit aerobic respiration and affect plant growth and development. Here, we demonstrate that the hypoxic microenvironment induced by active cell proliferation during the two-step plant regeneration process intrinsically represses the regeneration competence of the callus in Arabidopsis thaliana.

REGENOMICS: A web-based application for plant REGENeration-associated transcriptOMICS analyses.

In plants, differentiated somatic cells exhibit an exceptional ability to regenerate new tissues, organs, or whole plants. Recent studies have unveiled core genetic components and pathways underlying cellular reprogramming and tissue regeneration in plants. Although high-throughput analyses have led to key discoveries in plant regeneration, a comprehensive organization of large-scale data is needed to further enhance our understanding of plant regeneration.

Transcriptome comparison between pluripotent and non-pluripotent calli derived from mature rice seeds.

In vitro plant regeneration involves a two-step practice of callus formation and de novo organogenesis. During callus formation, cellular competence for tissue regeneration is acquired, but it is elusive what molecular processes and genetic factors are involved in establishing cellular pluripotency. To explore the mechanisms underlying pluripotency acquisition during callus formation in monocot plants, we performed a transcriptomic analysis on the pluripotent and non-pluripotent rice calli using RNA-seq.

JA-pretreated hypocotyl explants potentiate shoot regeneration in Arabidopsis.

Plant regeneration involves critical checkpoints including pluripotency acquisition and organogenesis. However, comprehensive understanding of the mechanisms that underlie plant regeneration remains limited. Here, we found that calli derived from jasmonate (JA)-pretreated hypocotyl explants exhibited increased rates of shoot regeneration.