Reactivation of an embryonic cardiac neural crest transcriptional profile during zebrafish heart regeneration
Creators
-
1.
University of California, Berkeley
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2.
California Institute of Technology
Abstract
During vertebrate development, the heart primarily arises from mesoderm, with crucial contributions from cardiac neural crest (CdNC) cells that migrate to the heart and form a variety of cardiovascular derivatives. Here, by integrating bulk and single cell RNA-seq with ATAC-seq, we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1, sox9a, tfap2a, and ets1. Notably, we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore, expression of all transcription factors from the migratory cardiac crest gene subcircuit are reactivated after injury at the wound edge. Together, our results uncover a developmental gene regulatory network that is important for CdNC fate determination, with key factors of the program reexpressed during regeneration.
Copyright and License
Copyright © 2025 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution- NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
Acknowledgement
We would like to thank Fish Facility staff at Caltech (David Mayorga and Ryan Fraser) and UC Berkeley (Tyler Mentley, Frances Campbell, and Lindsey Arenson) for zebrafish husbandry and care. We would also like to thank Diana Perez and Rochelle Diamond at the Caltech Flow Cytometry Cell Sorting Facility for help with FACS assistance. We would also like to acknowledge the Caltech Millard and Muriel Jacobs Genetics and Genomics Laboratory, in particular, Igor Antoshechkin and Vijaya Kumar for sequencing of our ATAC-seq and RNA-seq libraries. We would also like to thank Dr. Michael Piacentino and Dr. Ezgi Kunttas for dissection assistance for the TNC RNA-seq samples and Dr. Piacentino for consulting on image quantification. We would like to thank Eli Grossman for technical assistance in early gRNA design and synthesis. We would also like to thank Isaac Hilton-VanOsdall for his support in troubleshooting computational pipelines. Thank you to Dr. Iswar Hariharan and Dr. Lara Busby for providing us with feedback on the manuscript. This work was supported by an American Heart Association Career Development Award (854387), The Shurl and Kay Curci Foundation (051225), NIH K99/R00HD100587, and NIH DP2HL173858 awarded to M.L.M. Additional support came from NIH 1R01HL169287 awarded to M.E.B. A.K.H. was supported by NIH T32GM132022 and NIH F31HL17614. R.M.D-R was supported by T32 (T32GM148378) and NSF GRFP (2023360725).
Funding
This work was supported by an American Heart Association Career Development Award (854387), The Shurl and Kay Curci Foundation (051225), NIH K99/R00HD100587, and NIH DP2HL173858 awarded to M.L.M. Additional support came from NIH 1R01HL169287 awarded to M.E.B. A.K.H. was supported by NIH T32GM132022 and NIH F31HL17614. R.M.D-R was supported by T32 (T32GM148378) and NSF GRFP (2023360725).
Contributions
M.E.B. and M.L.M. designed research; R.M.D.-R., A.K.H., L.W.L., and M.L.M. performed research; M.E.B. and M.L.M. contributed new reagents/analytic tools; R.M.D.-R., A.K.H., L.W.L., J.K.M., M.E.B., and M.L.M. analyzed data; and R.M.D.-R., A.K.H., L.W.L., M.E.B., and M.L.M. wrote the paper.
Data Availability
The datasets generated in this study have been deposited in the Gene Expression Omnibus (GEO) and can be accessed as follows: single-cell RNA-seq [GSE287811] (73), bulk ATAC-seq [GSE287813] (74), and bulk RNA-seq [GSE287815] (75). Unprocessed czi files for all confocal images included in this manuscript can be found on Figshare (76). Code for data processing and analysis can be found on Github (77).
Code Availability
R. Dhillon-Richardson et al., DhillonRichardsonHaugan_PNAS2024. GitHub. https://github.com/Martik-Lab/DhillonRichardsonHaugan_PNAS2024. Deposited 12 November 2024.
Conflict of Interest
The authors declare no competing interests.
Supplemental Material
Supporting Information:
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dhillon-richardson-et-al-2025-reactivation-of-an-embryonic-cardiac-neural-crest-transcriptional-profile-during.pdf
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Additional details
Identifiers
- PMID
- 40531881
- PMCID
- PMC12207451
Funding
- American Heart Association
- 854387
- Shurl and Kay Curci Foundation
- 051225
- National Institutes of Health
- K99/R00HD100587
- National Heart Lung and Blood Institute
- DP2HL173858
- National Institutes of Health
- 1R01HL169287
- National Institutes of Health
- T32GM132022
- National Institutes of Health
- F31HL17614
- National Institutes of Health
- T32GM148378
- National Science Foundation
- 2023360725
Dates
- Submitted
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2024-11-13
- Accepted
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2025-05-05
- Available
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2025-06-18Published online
Caltech Custom Metadata
- Caltech groups
- Division of Biology and Biological Engineering (BBE)
- Publication Status
- Published