The m⁶A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis

Abstract

The epitranscriptomic mark -methyladenosine (mA) can be written, read, and erased via the action of a complex network of proteins. mA binding proteins read mA marks and transduce their downstream regulatory effects by altering RNA metabolic processes. The characterization of mA readers is an essential prerequisite for understanding the roles of mA in plants, but the identities of mA readers have been unclear. Here, we characterized the YTH-domain family protein ECT2 as an mA reader whose mA 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 mA 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 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 mA in RNA metabolism, as well as plant development and physiology.

Topologies of N6‐adenosine methylation (m6A) in land plant mitochondria and their putative effects on organellar gene expression

“…Global RNA‐seq analyses of the model plant A. thaliana indicated the presence of m 6 A modifications within many nuclear‐encoded mRNA transcripts (Zhong et al , ; Bodi et al , ; Shen et al , ; Růžička et al , ; Wei et al , ; Parker et al , ). These analyses further suggested that the organellar (i.e.…”

“…As in animals, the N 6 ‐methylation of adenosine residues in nuclear‐encoded mRNAs in land plants is positioned predominantly towards the 3′‐end of the transcript (Bodi et al , ; Dominissini et al , ; Chen and Liu, ; Luo et al , ; Ke et al , ; Wan et al , ; Burgess et al , ; Li et al , ; Scutenaire et al , ; Wei et al , ). This was also supported by Nanopore direct RNA sequencing of Arabidopsis plants (Parker et al , ).…”

“…This was also supported by Nanopore direct RNA sequencing of Arabidopsis plants (Parker et al , ). The significance of m 6 A is apparent in mutant plants with reduced levels of m 6 A that show embryogenesis defects and altered growth and developmental phenotypes (Zhong et al , ; Bodi et al , ; Wan et al , ; Shen et al , ; Růžička et al , ; Arribas‐Hernández et al , ; Chen et al , ; Li et al , ; Wei et al , ). Global m 6 A‐RIP‐seq analyses also indicated the presence of m 6 A within organellar (i.e.…”

N6‐methyladenosine regulatory machinery in plants: composition, function and evolution

“…Plants have more YTH domain proteins than other eukaryotes, including yeast, human and other mammals (Meyer and Jaffrey, ). For instance, 13 YTH domain proteins named ECT1‐12 and CPSF30 were found in Arabidopsis , which is significantly higher than that of the 5 YTH proteins identified in mammals (Meyer and Jaffrey, ; Wei et al ., ). The results showed that YTH proteins were widespread in land plants.…”

The Story Continues: Following the Fate of m6A Marks in the Eukaryotic Transcriptome

“…This modification regulates gene expression during a myriad of processes ranging from leaf and trichome development in Arabidopsis thaliana (Arribas-Hernández et al, 2018;Scutenaire et al, 2018;Wei et al, 2018) to cell fate determination in humans. These marks, which are deposited at specific mRNA sequences by m 6 A writers and removed by m 6 A erasers, recruit and anchor m 6 A-binding proteins (readers) that play vital roles in pre-mRNA splicing, mRNA degradation, and translation (reviewed in Meyer and Jaffrey, 2017).…”