Reprogramming of cells during embryonic transfating: overcoming a reprogramming block

“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 also are initially absent, as their specification depends on signaling from micromeres. Most mesoderm cells later return by transfating, but pigment cells do not. ScRNA-seq, 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 mesodermal 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 sequence of switches in gene regulatory states, and reprogramming fails if endogenous negative signals occur prior to positive signals in the replacement sequence. Overall design: 7 scRNA-seq samples capturing 7 time points over 18 hours of micromereless sea urchin development