Structural analyses of an RNA stability element interacting with poly(A)

Torabi, Seyed-Fakhreddin; Chen, Yen-Lin; Zhang, Kaiming; Wang, Jimin; DeGregorio, Suzanne J.; Vaidya, Anand T.; Su, Zhaoming; Pabit, Suzette A.; Chiu, Wah; Pollack, Lois; Steitz, Joan A.

doi:10.1073/pnas.2026656118

Structural analyses of an RNA stability element interacting with poly(A)

Journal Article · Mon Feb 22 00:00:00 EST 2021 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.2026656118· OSTI ID:1798368

^[1]; ^[2]; ^[3]; ^[1]; DeGregorio, Suzanne J. ^[1]; Vaidya, Anand T. ^[1]; ^[3]; ^[2]; ^[4]; ^[2]; Steitz, Joan A. ^[1]

Yale Univ., New Haven, CT (United States)
Cornell Univ., Ithaca, NY (United States)
Stanford Univ., CA (United States)
Stanford Univ., CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)

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. Finally, these findings are consistent with the recently solved crystal structure of a dENE+poly(A) complex [S.-F. Torabi et al., Science 371, eabe6523 (2021)]. Identification of additional modes of poly(A)–RNA interaction opens new venues for better understanding of poly(A) tail biology.

View Accepted Manuscript (DOE)

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1798368

Alternate ID(s):: OSTI ID: 1783764

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 14 Vol. 118; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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Structural analyses of an RNA stability element interacting with poly(A)

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