Polyadenylation Complex CFII Recognizes Downstream Cis‐element for Pre‐mRNA Polyadenylation Through Interaction with an RNA‐Binding Protein in Arabidopsis

Alternative polyadenylation of pre-mRNA generates mRNAs with alternative 3' ends, thereby increasing the complexity of the transcriptome and proteome. This process is carried out by pre-mRNA 3' end processing complexes, with the specificity and site selection of polyadenylation primarily defined by the interaction between these complexes and conserved pre-mRNA cis-elements. However, the cis-element recognized by the polyadenylation CFII complex and the downstream cis-element of the poly(A) site remain unknown. Here, FPA, a conserved Spen family RNA-binding protein, is identified to physically interacts with the CFII complex in Arabidopsis. FPA specifically binds to a GA-rich cis-element downstream of the proximal poly(A) site, which is required for the CFII complex to promote proximal poly(A) site usage and prevent 3' extension. Thus, the CFII complex recognizes the downstream cis-element of the poly(A) site through its interaction with FPA, highlighting the role of RNA-binding proteins as accessory factors in alternative polyadenylation.