Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536.
HHMI, Yale University School of Medicine, New Haven, CT 06536.
Proc Natl Acad Sci U S A. 2021 Apr 6;118(14). doi: 10.1073/pnas.2026656118.
Cis-acting RNA elements are crucial for the regulation of polyadenylated RNA stability. The element for nuclear expression (ENE) contains a U-rich internal loop flanked by short helices. An ENE stabilizes RNA by sequestering the poly(A) tail via formation of a triplex structure that inhibits a rapid deadenylation-dependent decay pathway. Structure-based bioinformatic studies identified numerous ENE-like elements in evolutionarily diverse genomes, including a subclass containing two ENE motifs separated by a short double-helical region (double ENEs [dENEs]). Here, the structure of a dENE derived from a rice transposable element (TWIFB1) before and after poly(A) binding (∼24 kDa and ∼33 kDa, respectively) is investigated. We combine biochemical structure probing, small angle X-ray scattering (SAXS), and cryo-electron microscopy (cryo-EM) to investigate the dENE structure and its local and global structural changes upon poly(A) binding. Our data reveal 1) the directionality of poly(A) binding to the dENE, and 2) that the dENE-poly(A) interaction involves a motif that protects the 3'-most seven adenylates of the poly(A). Furthermore, we demonstrate that the dENE does not undergo a dramatic global conformational change upon poly(A) binding. These findings are consistent with the recently solved crystal structure of a dENE+poly(A) complex [S.-F. Torabi , 371, eabe6523 (2021)]. Identification of additional modes of poly(A)-RNA interaction opens new venues for better understanding of poly(A) tail biology.
顺式作用 RNA 元件对于聚腺苷酸化 RNA 稳定性的调节至关重要。核表达元件（ENE）包含一个富含 U 的内部环，两侧是短螺旋。ENE 通过形成抑制快速脱腺苷酸化依赖性衰减途径的三聚体结构来隔离聚（A）尾，从而稳定 RNA。基于结构的生物信息学研究在进化上多样化的基因组中鉴定了许多 ENE 样元件，包括一个包含两个 ENE 基序的子类，它们之间有一个短的双链区（双 ENE [dENE]）。在此，研究了来自水稻转座元件（TWIFB1）的 dENE 在结合聚（A）前后的结构（分别约为 24 kDa 和 33 kDa）。我们结合生化结构探测、小角度 X 射线散射（SAXS）和冷冻电镜（cryo-EM）来研究 dENE 的结构及其在结合聚（A）后的局部和整体结构变化。我们的数据揭示了 1）聚（A）结合到 dENE 的方向性，以及 2）dENE-聚（A）相互作用涉及一个保护聚（A）的 3'-末端七个腺嘌呤的基序。此外，我们证明 dENE 在结合聚（A）后不会发生剧烈的整体构象变化。这些发现与最近解决的 dENE+poly(A) 复合物晶体结构一致 [S.-F. Torabi, 371, eabe6523 (2021)]。鉴定额外的聚（A）-RNA 相互作用模式为更好地理解聚（A）尾生物学开辟了新途径。
