Project description: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.
2025-09-01 | GSE305723 | GEO
Project description:Assembly and annotation of complete mitochondrial genome of Kadsura japonica
Project description: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.
Project description: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.
Project description: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.
Project description:To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2