Targeted RNA N6-Methyladenosine Demethylation Controls Cell Fate Transition in Human Pluripotent Stem Cells

Deficiency of the N6-methyladenosine (m6A) methyltransferase complex results in global reduction of m6A abundance and defective cell development in embryonic stem cells (ESCs). However, it's unclear whether regional m6A methylation would affect cell fate decisions due to the inability to modulate individual m6A modification in ESCs with precise temporal control. Here, we develop a targeted RNA m6A erasure (TRME) system to achieve site-specific demethylation of RNAs in human ESCs (hESCs). TRME, in which a stably transfected, doxycycline-inducible dCas13a is fused to the catalytic domain of ALKBH5, can precisely and reversibly demethylate the targeted m6A site of mRNA and increase mRNA stability with limited off-target effects. We further demonstrate that temporal m6A erasure on a single site of SOX2 is sufficient to control the differentiation of hESCs. This study provides a versatile toolbox to reveal the function of individual m6A modification in hESCs, enabling cell fate control studies at the epitranscriptional level. Overall design: Examination of m6A modification variation in the TRME hESCs treated with doxycycline or not.