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PMID: 25999316 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.

RNA (New York, N.Y.) ·Vol. 21 ·No. 7 ·2015-07-00 ·Pages 1274-85

Kutchko KM, Sanders W, Ziehr B, Phillips G, Solem A, Halvorsen M, Weeks KM, Moorman N, Laederach A

Abstract

Folding to a well-defined conformation is essential for the function of structured ribonucleic acids (RNAs) like the ribosome and tRNA. Structured elements in the untranslated regions (UTRs) of specific messenger RNAs (mRNAs) are known to control expression. The importance of unstructured regions adopting multiple conformations, however, is still poorly understood. High-resolution SHAPE-directed Boltzmann suboptimal sampling of the Homo sapiens Retinoblastoma 1 (RB1) 5' UTR yields three distinct conformations compatible with the experimental data. Private single nucleotide variants (SNVs) identified in two patients with retinoblastoma each collapse the structural ensemble to a single but distinct well-defined conformation. The RB1 5' UTRs from Bos taurus (cow) and Trichechus manatus latirostris (manatee) are divergent in sequence from H. sapiens (human) yet maintain structural compatibility with high-probability base pairs. SHAPE chemical probing of the cow and manatee RB1 5' UTRs reveals that they also adopt multiple conformations. Luciferase reporter assays reveal that 5' UTR mutations alter RB1 expression. In a traditional model of disease, causative SNVs disrupt a key structural element in the RNA. For the subset of patients with heritable retinoblastoma-associated SNVs in the RB1 5' UTR, the absence of multiple structures is likely causative of the cancer. Our data therefore suggest that selective pressure will favor multiple conformations in eukaryotic UTRs to regulate expression.

Keywords
SHAPE UTR covariation retinoblastoma riboSNitch
MeSH Terms
5' Untranslated Regions Humans Phylogeny Protein Conformation Retinoblastoma Protein/genetics,physiology Structure-Activity Relationship
Chemicals
5' Untranslated Regions Retinoblastoma Protein
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Kutchko Katrina M
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Sanders Wes
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
Ziehr Ben
Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Phillips Gabriela
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
Solem Amanda
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
Halvorsen Matthew
Institute for Genomic Medicine, Columbia University Medical Center, New York, New York 10032, USA.
Weeks Kevin M
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
Moorman Nathaniel
Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
Laederach Alain
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA alain@unc.edu.
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Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1469-9001
DOI
10.1261/rna.049221.114
Email
alain@unc.edu
Published
2015-07-00
Epub
2015-00-21
Pages
1274-85
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC4478346
Subset
IM
Grants
NHGRI NIH HHS · R01 HG008133 · United States
NHLBI NIH HHS · R01 HL111527 · United States
NIGMS NIH HHS · R01GM064803 · United States
NIGMS NIH HHS · R01 GM064803 · United States
NIGMS NIH HHS · R01 GM101237 · United States
NIAID NIH HHS · R01 AI103311 · United States
External Links
PubMed source DOI: 10.1261/rna.049221.114 PMC Full Text View journal details
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