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RNA. 2015 Jul;21(7):1274-85. doi: 10.1261/rna.049221.114. Epub 2015 May 21.

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

Author information

1
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.
2
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
3
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.
4
Institute for Genomic Medicine, Columbia University Medical Center, New York, New York 10032, USA.
5
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
6
Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA alain@unc.edu.

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

PMID:
25999316
PMCID:
PMC4478346
DOI:
10.1261/rna.049221.114
[Indexed for MEDLINE]
Free PMC Article

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