RNA stabilization by a poly(A) tail 3ʹ-end binding pocket and other modes of poly(A)-RNA interaction

Poly(A) tail addition to the 3ʹ end of a wide range of RNAs is a highly conserved modification that plays a central role in cellular RNA function. Elements for nuclear expression (ENEs) are cis-acting RNA elements that stabilize poly(A) tails by sequestering them in RNA triplex structures. A 2.89-Å resolution crystal structure of a double ENE from a rice hAT transposon mRNA complexed with poly(A)28 reveals multiple modes of interaction with poly(A), including major-groove triple helices, extended minor-groove interactions with RNA double helices, a quintuple-base motif that transitions poly(A) from minor-groove associations to major-groove triple helices, and a poly(A) 3ʹ-end binding pocket. Our findings both expand the repertoire of motifs involved in long-range RNA interactions and provide insights into how polyadenylation can protect an RNA’s extreme 3ʹ end.