2023-10-12
Whole-body regeneration of planarians is a natural wonder but how it occurs remains elusive. It requires coordinated responses from each cell in the remaining tissue with spatial awareness to regenerate new cells and missing body parts. While previous studies identified new genes essential to regeneration, a more efficient screening approach that can identify regeneration-associated genes in the spatial context is needed. Here, we present a comprehensive three-dimensional spatiotemporal transcriptomic landscape of planarian regeneration. We describe a pluripotent neoblast subtype, and show that depletion of its marker gene makes planarians more susceptible to sub-lethal radiation. Furthermore, we identified spatial gene expression modules essential for tissue development. Functional analysis of hub genes in spatial modules, such as plk1, shows their important roles in regeneration. Our three-dimensional transcriptomic atlas provides a powerful tool for deciphering regeneration and identifying homeostasis-related genes, and provides a publicly available online spatiotemporal analysis resource for planarian regeneration research.
Publication:
Nature Communications 14, 3205 (2023).
https://doi.org/10.1038/s41467-023-39016-0
Author:
Guanshen Cui
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
Kangning Dong
NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
Jia-Yi Zhou
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
Shang Li
NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
Ying Wu
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
Qinghua Han
NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
Bofei Yao
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
Qunlun Shen
NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
Yong-Liang Zhao
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
University of Chinese Academy of Sciences, Beijing, China
Ying Yang
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China
Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
Jun Cai
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
University of Chinese Academy of Sciences, Beijing, China
Shihua Zhang
NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
Email: zsh@amss.ac.cn
Yun-Gui Yang
CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
China National Center for Bioinformation, Beijing, 100101, China
Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China
Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
