Single-Nucleotide m ⁶ A Mapping Uncovers Redundant YTHDF Function in Planarian Progenitor Fate Selection

Cell fate decisions require tight regulation of gene expression. In planarians—highly regenerative flatworms—the mRNA modification N ⁶ -methyladenosine (m ⁶ A) modulates progenitor production and fate. However, the mechanisms governing m ⁶ A deposition in the planarian transcriptome—and the role of their expanded family of YTHDF m ⁶ A reader proteins in orchestrating biological functions—remain unclear. Here, we generated the first single-nucleotide resolution map of m ⁶ A in planarians, and revealed that simple sequence rules guide m ⁶ A deposition, facilitating the flexible evolutionary gain and loss of these marks. Functional analyses of the five planarian m ⁶ A readers revealed that while individual reader expression is dispensable, together, the planarian readers regulate the production of specific progenitor lineages and overall body size. Collectively, our findings uncover a robust, redundant regulatory architecture, characterized by multiple m ⁶ A sites per gene and coordinated m ⁶ A reader expression. This architecture is essential for proper lineage resolution and provides insights into the evolutionary dynamics of the m ⁶ A landscape.