Abstract

Nonsense-mediated decay (NMD) is a posttranscriptional surveillance mechanism in eukaryotes that recognizes and degrades transcripts with premature translation-termination codons (PTCs). The RNA polymerase II C-terminal domain phosphatase-like protein FIERY2 (FRY2, also known as CPL1) plays multiple roles in RNA processing in Arabidopsis. Here, we found that FRY2 interacts with two NMD factors, eIF4AIII and UPF3, and is required for the dephosphorylation of eIF4AIII, which retains eIF4AIII in the nucleus and limits its cytoplasmic accumulation. By analyzing newly generated RNA-seq data combing with quantitative RT-PCR validation, we identified that a subset of alternatively spliced transcripts and 5'-extended mRNAs with NMD-eliciting features were commonly accumulated in the fry2-1 mutant, cycloheximide-treated wild type and upf3 mutant plants, indicating that FRY2 is essential for the degradation of these NMD transcripts.