The Cre–loxP recombination system is the most widely used technology for in vivo tracing of stem or progenitor cell lineages. The precision of this genetic system largely depends on the specificity of Cre recombinase expression in targeted stem or progenitor cells. However, Cre expression in nontargeted cell types can complicate the interpretation of lineage-tracing studies and has caused controversy in many previous studies. Here we describe a new genetic lineage tracing system that incorporates the Dre–rox recombination system to enhance the precision of conventional Cre–loxP-mediated lineage tracing. The Dre–rox system permits rigorous control of Cre–loxP recombination in lineage tracing, effectively circumventing potential uncertainty of the cell-type specificity of Cre expression. Using this new system we investigated two topics of recent debates—the contribution of c-Kit+ cardiac stem cells to cardiomyocytes in the heart and the contribution of Sox9+ hepatic progenitor cells to hepatocytes in the liver. By overcoming the technical hurdle of nonspecific Cre–loxP-mediated recombination, this new technology provides more precise analysis of cell lineage and fate decisions and facilitates the in vivo study of stem and progenitor cell plasticity in disease and regeneration.

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We thank B. Wu, G. Chen, Z. Weng and A. Huang for the animal husbandry and W. Bian for technical help. We thank H. Zeng at Allen Institute for sharing mouse lines and K. Anastassiadis for valuable suggestions and insightful advice on this study. We thank Shanghai Model Organisms Center, Inc. (SMOC) and Nanjing Biomedical Research Institute of Nanjing University for the generation of mouse lines. This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (grant no. XDB19000000; B.Z.), the National Science Foundation of China (grant no. 31730112 (B.Z.), 91639302 (B.Z.), 31625019 (B.Z.), 31571503 (X.T.), 31501172 (H. Zhang), 31601168 (Q.L.) and 31701292 (L.H.)), the National Key Research and Development Program of China (grant no. 2017YFC1001303 (L.H.) and 2016YFC1300600 (X.T.)), the Youth Innovation Promotion Association of CAS (award no. 2015218; X.T.), the Key Project of Frontier Sciences of CAS (grant no. QYZDB-SSW-SMC003; B.Z.), the International Cooperation Fund of CAS (B.Z.), the National Program for Support of Top-notch Young Professionals (B.Z.), the Shanghai Science and Technology Commission (grant no. 17ZR1449600 (B.Z.) and 17ZR1449800 (X.T.)), the Young Elite Scientists Sponsorship Program by the China Association for Science and Technology (Q.L. and L.H.), the Shanghai Yangfan Project (award no. 15YF1414000 (H. Zhang) and 16YF1413400 (L.H.)) and Rising-Star Program (grant no.15QA1404300; X.T.), the China Postdoctoral Science Foundation (Y.W., Q.L. and J.T.), the President Fund of Shanghai Institutes for Biological Sciences (SIBS) (B.Z.), Astrazeneca (B.Z.), Sanofi-SIBS Fellowship (X.T. and L.H.), Boehringer Ingelheim (B.Z.) and a Royal Society–Newton Advanced Fellowship (B.Z.).

Author information


  1. State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Shanghai, China.

    • Lingjuan He
    • , Yan Li
    • , Yi Li
    • , Wenjuan Pu
    • , Xiuzhen Huang
    • , Xueying Tian
    • , Yue Wang
    • , Hui Zhang
    • , Qiaozhen Liu
    • , Libo Zhang
    • , Huan Zhao
    • , Juan Tang
    • , Hongbin Ji
    •  & Bin Zhou
  2. Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.

    • Lingjuan He
    • , Yan Li
    • , Yi Li
    • , Wenjuan Pu
    • , Xiuzhen Huang
    • , Xueying Tian
    • , Yue Wang
    • , Hui Zhang
    • , Qiaozhen Liu
    • , Libo Zhang
    • , Huan Zhao
    • , Juan Tang
    •  & Bin Zhou
  3. School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

    • Hongbin Ji
    •  & Bin Zhou
  4. Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China.

    • Dongqing Cai
    •  & Bin Zhou
  5. State Key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Disease, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin, China.

    • Zhibo Han
    •  & Zhongchao Han
  6. State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

    • Yu Nie
    •  & Shengshou Hu
  7. Bioscience Heart Failure, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.

    • Qing-Dong Wang
  8. Shanghai Model Organisms Center, Inc., Shanghai, China.

    • Ruilin Sun
    •  & Jian Fei
  9. National Institute of Biological Sciences, Beijing, China.

    • Fengchao Wang
    •  & Ting Chen
  10. Zhongshan Hospital, Fudan University, Shanghai, China.

    • Yan Yan
  11. International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

    • Hefeng Huang
  12. Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts, USA and Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA.

    • William T Pu
  13. Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, Tianjin, China.

    • Bin Zhou


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L.H. and B.Z. designed the study, performed experiments and analyzed the data; Yan Li, Yi Li, W.P., X.H., X.T., Y.W., H. Zhang, Q.L., L.Z., H. Zhao and J.T. bred the mice and performed experiments; D.C., H.J., Zhibo Han, Zhongchao Han, Y.N., S.H., Q.-D.W., R.S., J.F., Y.Y. and H.H. analyzed data, provided technical support and edited the manuscript; F.W. and T.C. provided mouse lines; W.T.P. provided intellectual input and edited the manuscript; B.Z. conceived and supervised the study, analyzed the data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Bin Zhou.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11 & Supplementary Table 1

  2. 2.

    Life Sciences Reporting Summary