Regulatory Mechanisms of Alternative Polyadenylation in Plants: Roles of Poly(A) Protein Complexes in Transcriptome Plasticity

ABSTRACT

Transcriptome plasticity is a key driver of proteome diversity, enabling organisms to finely tune gene expression in response to developmental cues and environmental stimuli, essential features for sessile plants facing constant challenges. Among the co‐transcriptional processes contributing to this plasticity—such as alternative transcription start sites and alternative splicing—alternative polyadenylation (APA) plays a particularly prominent role, affecting 60%–70% of plant genes. Despite its prevalence, the molecular mechanisms guiding APA and its regulation remain incompletely understood. This review synthesizes recent advances in our understanding of how polyadenylation protein complexes—including Cleavage and Polyadenylation Specificity Factors (CPSF), Cleavage stimulation Factors (CstF), and Cleavage Factors (CF)—interact with cis‐regulatory elements to determine poly(A) site choice. We highlight the coordinated actions of these protein families and their dynamic regulation across tissues, developmental stages, and environmental conditions. Furthermore, we propose a conceptual model of the regulatory network involving RNA‐protein and protein–protein interactions that govern APA in plants. Deciphering these molecular networks offers promising avenues for targeted manipulation of APA to enhance crop resilience and productivity. Understanding the spatial and temporal regulation of polyadenylation machinery may ultimately enable precision control of gene expression in molecular breeding and agricultural biotechnology.