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Title: Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels

Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. Exploring the structured 3' untranslated region (UTR) of a viral RNA, we discovered that different contexts of the 3'-UTR confer different abilities to enhance translation of an associated open reading frame. In one context, ribosome-induced conformational changes in a ‘sensor’ RNA domain affect a separate RNA ‘functional’ domain, altering translation efficiency. The structure of the entire 3'-UTR reveals that structurally distinct domains use a spine of continuously stacked bases and a strut-like linker to create a conduit for communication within the higher-order architecture. Furthermore, this 3'-UTR RNA illustrates how RNA can use programmed conformational changes to sense the translation status of an upstream open reading frame, then create a tuned functional response by communicating that information to other RNA elements.
Authors:
 [1] ;  [2] ;  [2] ;  [3] ;  [4] ; ORCiD logo [4] ; ORCiD logo [2]
  1. Univ. of Colorado, Denver, CO (United States); Univ. of Colorado Denver School of Medicine, Aurora, CO (United States)
  2. Univ. of Colorado Denver School of Medicine, Aurora, CO (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Stanford Univ., Stanford, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1493274

Hartwick, Erik W., Costantino, David A., MacFadden, Andrea, Nix, Jay C., Tian, Siqi, Das, Rhiju, and Kieft, Jeffrey S.. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. United States: N. p., Web. doi:10.1038/s41467-018-07542-x.
Hartwick, Erik W., Costantino, David A., MacFadden, Andrea, Nix, Jay C., Tian, Siqi, Das, Rhiju, & Kieft, Jeffrey S.. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. United States. doi:10.1038/s41467-018-07542-x.
Hartwick, Erik W., Costantino, David A., MacFadden, Andrea, Nix, Jay C., Tian, Siqi, Das, Rhiju, and Kieft, Jeffrey S.. 2018. "Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels". United States. doi:10.1038/s41467-018-07542-x. https://www.osti.gov/servlets/purl/1493274.
@article{osti_1493274,
title = {Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels},
author = {Hartwick, Erik W. and Costantino, David A. and MacFadden, Andrea and Nix, Jay C. and Tian, Siqi and Das, Rhiju and Kieft, Jeffrey S.},
abstractNote = {Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. Exploring the structured 3' untranslated region (UTR) of a viral RNA, we discovered that different contexts of the 3'-UTR confer different abilities to enhance translation of an associated open reading frame. In one context, ribosome-induced conformational changes in a ‘sensor’ RNA domain affect a separate RNA ‘functional’ domain, altering translation efficiency. The structure of the entire 3'-UTR reveals that structurally distinct domains use a spine of continuously stacked bases and a strut-like linker to create a conduit for communication within the higher-order architecture. Furthermore, this 3'-UTR RNA illustrates how RNA can use programmed conformational changes to sense the translation status of an upstream open reading frame, then create a tuned functional response by communicating that information to other RNA elements.},
doi = {10.1038/s41467-018-07542-x},
journal = {Nature Communications},
number = 1,
volume = 9,
place = {United States},
year = {2018},
month = {11}
}

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