m ⁶Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression

Abstract

The study uncovers the pivotal role of PCIF1-mediated m ⁶Am RNA modification in ciliogenesis. PCIF1 negatively regulates ciliation by modulating BICD2 protein levels via m ⁶Am catalytic activity, influencing mRNA stability and translation efficiency. These findings elucidate a fundamental mechanism in ciliogenesis regulation.

Abstract

N6, 2′-O-dimethyladenosine (m ⁶Am) is a widespread RNA modification catalyzed by the methyltransferase PCIF1 (phosphorylated CTD interacting factor 1). Despite its prevalence, the biological functions of m ⁶Am in RNA remain largely elusive. Here, we report a critical role of PCIF1-dependent m ⁶Am RNA modification in ciliogenesis in RPE-1 cells. Our findings demonstrate that PCIF1 acts as a negative regulator of ciliation through its m ⁶Am methyltransferase activity. A quantitative proteomic analysis identifies BICD2 as a downstream target of PCIF1, with PCIF1 depletion resulting in a significant increase in BICD2 levels. BICD2 depletion leads to a significant reduction in ciliation. Crucially, the ciliary phenotype in PCIF1-depleted cells is reversed upon BICD2 knockdown. Further investigations reveal that PCIF1 regulates BICD2 protein levels through its m ⁶Am catalytic activity, which reduces the stability and translation efficiency of BICD2 mRNA. Single-base resolution LC-MS analysis identifies the m ⁶Am site on BICD2 mRNA modified by PCIF1. These findings establish the essential involvement of PCIF1-dependent m ⁶Am modification in ciliogenesis.