m6A is required for resolving progenitor identity during planarian stem cell differentiation

Regeneration and tissue homeostasis require accurate production of missing cell lineages. Cell production is driven by changes to gene expression, which is shaped by multiple layers of regulation. Here, we find that the ubiquitous mRNA base‐modification, m6A, is required for proper cell fate choice and cellular maturation in planarian stem cells (neoblasts). We mapped m6A‐enriched regions in 7,600 planarian genes and found that perturbation of the m6A pathway resulted in progressive deterioration of tissues and death. Using single‐cell RNA sequencing of >20,000 cells following perturbation of the m6A pathway, we identified an increase in expression of noncanonical histone variants, and that inhibition of the pathway resulted in accumulation of undifferentiated cells throughout the animal in an abnormal transcriptional state. Analysis of >1,000 planarian gene expression datasets revealed that the inhibition of the chromatin modifying complex NuRD had almost indistinguishable consequences, unraveling an unappreciated link between m6A and chromatin modifications. Our findings reveal that m6A is critical for planarian stem cell homeostasis and gene regulation in tissue maintenance and regeneration. Synopsis Whether biochemical mRNA modification regulates somatic stem cell function remains poorly understood. Here, genome‐wide mapping shows requirement of N6‐methylation of adenosine (m6A) for fate specification of flatworm stem cells, neoblasts, and suggests unexpected functional association between m6A and chromatin modification. m6A mRNA modification is widespread in the planarian transcriptome and required for cell fate progression of planarian neoblasts. Depletion of m6A pathway components results in reduced body size, impaired regeneration, and body‐wide emergence of undifferentiated cells with abnormal transcriptional state. Planarian gene expression datasets reveal remarkably similar molecular consequences upon inhibition of the NuRD chromatin remodeling complex. Graphical Abstract Somatic stem cell specification and regeneration of the flatworm are safeguarded by the m6A mRNA modification pathway.