Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration

The blastema is key to forming complete tissues in regenerating Dugesia japonica (D. japonica). However, the dynamic changes in cellular compositions and transcription landscapes in blastema during regeneration are understudied. Here, through genome reannotation, 3D spatial transcriptome construction, scRNA-seq and scATAC-seq analyses of changes in gene expression and chromatin structures, we delineated key transcription factors regulating the developmental trajectories of major cell clusters in the regenerating head. Importantly, we found that the T-cell factor 4 positive (DjTcf4+) cells highly accumulated at wound areas, and its gene network is critical for proper timing of development during regeneration in multiple progenitor cells. Depletion of DjTcf4 and its target genes led to singular eye and/or dull tail phenotypes and delayed regeneration. Taken together, we built multi-omics atlases in D. japonica and revealed noncanonical function of the DjTcf4 network in developmental pattern formation, laying a foundation for studies of regeneration in D. japonica. Overall design: Examine spital gene expression profiles of head blastema animals by 10X Visium platform.