ABSTRACT
Regulative development, demonstrated by many animal embryos, is the ability to replace missing cells or parts. The underlying molecular mechanism(s) of that ability is not well understood. If sea urchin micromeres (skeletogenic cell progenitors) are removed at the 16-cell stage, early endoderm initiates a sequential switch in cell fates, called transfating. Without micromeres, other mesoderm cells are absent as well, because their specification depends on signaling from micromeres. Most mesoderm cells later return by transfating, but pigment cells do not. Single-cell RNA sequencing, tracked over time, reveals the reprogramming sequence of those replacements. Beginning with an early endoderm specification state, cells progress through endomesoderm, then mesoderm, and finally distinct skeletogenic and blastocoelar cell specification states emerge, but pigment cells do not. Rescue of pigment cells was found to be a consequence of signal timing: if Delta is expressed prior to Nodal, pigment cells return. Thus, transfating operates through a series of gene regulatory state transitions, and reprogramming fails if endogenous negative signals occur prior to positive signals in the reprogramming sequence.
Footnotes
Author contributions
Conceptualization: G.S., G.A.W., D.R.M.; Methodology: A.B., E.M., A.J.M., A.A., G.S., D.R.M.; Software: A.B., A.J.M., A.A., G.S.; Validation: E.M., D.R.M.; Formal analysis: A.B., E.M., A.J.M., A.A., G.S., D.R.M.; Investigation: A.B., E.M., G.A.W., D.R.M.; Resources: A.J.M., G.S., G.A.W., D.R.M.; Data curation: A.B., A.J.M., A.A.; Writing - original draft: D.R.M.; Writing - review & editing: A.B., G.A.W., D.R.M.; Visualization: A.B., G.A.W., D.R.M.; Supervision: G.A.W., D.R.M.; Project administration: D.R.M.; Funding acquisition: G.A.W., D.R.M.
Funding
Support for this project was provided by National Institutes of Health (RO1 HD 14483 to D.R.M., T32 HD040372 to A.J.M.); the National Science Foundation (IOS-1457305 to G.A.W., DGE-1644868 to A.J.M.); a Career Award at the Scientific Interface from the Burroughs Wellcome Fund (G.S.), a Natural Sciences and Engineering Research Council of Canada Discovery grant (G.S.), the New Frontiers in Research Fund and an Exploration grant funded by the Government of Canada (G.S.), and a Genome Science and Technology summer student scholarship from the University of British Columbia, Canada (A.A.). Deposited in PMC for release after 12 months.
Data availability
The DNA sequencing data have been deposited in Gene Expression Omnibus under accession number GSE277519. Precomputed data and scripts are accessible at https://zenodo.org/records/14051567 and https://github.com/wodanaz/Micromereless.
The people behind the papers
This article has an associated ‘The people behind the papers' interview with some of the authors.
