Single-Nucleotide m6A Mapping Uncovers Redundant YTHDF Function in Planarian Progenitor Fate Selection

Abstract

Cell fate decisions require tight regulation of gene expression. In planarians--highly regenerative flatworms--the mRNA modification N6-methyladenosine (m6A) modulates progenitor production and fate. However, the mechanisms governing m6A deposition in the planarian transcriptome--and the role of their expanded family of YTHDF m6A reader proteins in orchestrating biological functions--remain unclear. Here, we generated the first single-nucleotide resolution map of m6A in planarians, and revealed that simple sequence rules guide m6A deposition, facilitating the flexible evolutionary gain and loss of these marks. Functional analyses of the five planarian m6A 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 m6A sites per gene and coordinated m6A reader expression. This architecture is essential for proper lineage resolution and provides insights into the evolutionary dynamics of the m6A landscape.