A single-cell transcriptome atlas reveals the trajectory of early cell fate transition during callus induction in Arabidopsis

The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement.This developmental process incorporates a series of cell fate transitions and reprogramming.However,our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited.Here,we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0,1,and 4 days,and the construction of a detailed single-cell transcriptional atlas of the callus induction process.We identify the cell types responsible for initiating the early callus:lateral root primordium-initiating(LRPI)-like cells and quiescent center(QC)-like cells.LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia.We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells.QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration.We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions.Overall,our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation,significantly improving our understanding of callus formation.

The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases

Cell fate transition is a fascinating process involving complex dynamics of three-dimensional(3D)chromatin organization and phase separation,which play an essential role in cell fate decision by regulating gene expression.Phase separation is increasingly being considered a driving force of chromatin folding.In this review,we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure.In addition,we discuss current advances in understanding how phase separation contributes to physical and functional enhancerpromoter contacts.We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions,and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation.