# Single-nucleotide m⁶A mapping uncovers redundant YTHDF function in planarian progenitor fate selection

## TL;DR

This study maps mRNA modifications in flatworms and finds that multiple proteins work together to control cell fate and body size.

## Contribution

The first single-nucleotide resolution map of m⁶A in planarians reveals redundant YTHDF function in progenitor fate selection.

## Key findings

- Single-nucleotide m⁶A mapping shows conserved yet species-tuned motif types in planarian RNAs.
- Combined depletion of YTHDF proteins disrupts progenitor lineage production and causes body size reduction.
- YTHDF proteins act redundantly, with their coordinated expression essential for proper cell fate control.

## 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 YTHDF planarian m⁶A readers revealed that while individual reader expression is dispensable, together, the planarian YTHDF proteins regulate the production of specific progenitor lineages and overall body size. Collectively, our findings uncover a robust, redundant regulatory architecture for cell fate control in planarians, 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.

The sequence rules and regulators governing m⁶A deposition on mRNAs in regenerative flatworms remain unclear. Here, single-nucleotide resolution mapping of m6A transcriptome marks in Schmidtea mediterranea reveals buffered and redundant roles of YTHDF readers in cell fate and tissue maintenance.

A single-nucleotide m6A atlas of planarian RNAs resolves two installation motif types that are conserved, yet species-tuned.YTHDFs are co-expressed and act redundantly. Only combined depletion perturbs production of specific progenitor lineages.Instead of depleting stem cells, combined YTHDF loss produces a novel, aberrant cell state in specific lineages, accompanied by body size reduction.Reader dosage and m⁶A-target architecture jointly set progenitor fate bias, exposing a buffered-yet-specialized m⁶A control layer.

A single-nucleotide m6A atlas of planarian RNAs resolves two installation motif types that are conserved, yet species-tuned.

YTHDFs are co-expressed and act redundantly. Only combined depletion perturbs production of specific progenitor lineages.

Instead of depleting stem cells, combined YTHDF loss produces a novel, aberrant cell state in specific lineages, accompanied by body size reduction.

Reader dosage and m⁶A-target architecture jointly set progenitor fate bias, exposing a buffered-yet-specialized m⁶A control layer.

Tissue maintenance and cell fate of regenerative flatworms are shaped by combined activity of YTHDF m⁶A mRNA modification readers.