The m ⁶ A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis

Abstract

The epitranscriptomic mark <i>N</i>⁶-methyladenosine (m⁶A) can be written, read, and erased via the action of a complex network of proteins. m⁶A binding proteins read m⁶A marks and transduce their downstream regulatory effects by altering RNA metabolic processes. The characterization of m⁶A readers is an essential prerequisite for understanding the roles of m⁶A in plants, but the identities of m⁶A readers have been unclear. Here, we characterized the YTH-domain family protein ECT2 as an <i>Arabidopsis thaliana</i> m⁶A reader whose m⁶A binding function is required for normal trichome morphology. We developed the formaldehyde cross-linking and immunoprecipitation method to identify ECT2-RNA interaction sites at the transcriptome-wide level. This analysis demonstrated that ECT2 binding sites are strongly enriched in the 3' untranslated regions (3' UTRs) of target genes and led to the identification of a plant-specific m⁶A motif. Sequencing analysis suggested that ECT2 plays dual roles in regulating 3' UTR processing in the nucleus and facilitating mRNA stability in the cytoplasm. Disruption of <i>ECT2</i> accelerated the degradation of three ECT2 binding transcripts related to trichome morphogenesis, thereby affecting trichome branching. The results shed light on the underlying mechanisms of the roles of m⁶A in RNA metabolism, as well as plant development and physiology.