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TitleStructural analyses of an RNA stability element interacting with poly(A).
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 118, Issue 14, Year 2021
Publish dateApr 6, 2021
AuthorsSeyed-Fakhreddin Torabi / Yen-Lin Chen / Kaiming Zhang / Jimin Wang / Suzanne J DeGregorio / Anand T Vaidya / Zhaoming Su / Suzette A Pabit / Wah Chiu / Lois Pollack / Joan A Steitz /
PubMed AbstractCis-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 ...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.
External linksProc Natl Acad Sci U S A / PubMed:33785601 / PubMed Central
MethodsEM (single particle)
Resolution5.6 - 8.7 Å
Structure data

23401

7ljy

EMDB-23401, PDB-7ljy:
Cryo-EM structure of the B dENE construct complexed with a 28-mer poly(A)
Method: EM (single particle) / Resolution: 5.6 Å

EMDB-23402:
Cryo-EM structure of the B dENE construct without poly(A)
Method: EM (single particle) / Resolution: 8.7 Å

Source
  • oryza sativa (Asian cultivated rice)
  • synthetic construct (others)
KeywordsRNA / RNA triple helix / RNA stability / poly(A) / SAXS and cryo-EM

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