title: Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.
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.
authors.affiliation: 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.
authors.forename: Katrina M
authors.initials: KM
authors.lastname: Kutchko
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
authors.forename: Wes
authors.initials: W
authors.lastname: Sanders
authors.affiliation: 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.
authors.forename: Ben
authors.initials: B
authors.lastname: Ziehr
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Phillips
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: Solem
authors.affiliation: Institute for Genomic Medicine, Columbia University Medical Center, New York, New York 10032, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Halvorsen
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Weeks
authors.affiliation: 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.
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Moorman
authors.affiliation: Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA alain@unc.edu.
authors.forename: Alain
authors.initials: A
authors.lastname: Laederach
mesh_terms: D020121:5' Untranslated Regions; D006801:Humans; D010802:Phylogeny; D011487:Protein Conformation; D016160:Retinoblastoma Protein / Q000235:genetics / Q000502:physiology*; D013329:Structure-Activity Relationship
chemical_list: D020121:5' Untranslated Regions; D016160:Retinoblastoma Protein
keywords: SHAPE; UTR; covariation; retinoblastoma; riboSNitch