Consistent global structures of complex RNA states through multidimensional chemical mapping

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm reso...

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Bibliographic Details
Published in:eLife 2015-06, Vol.4, p.e07600-e07600
Main Authors: Cheng, Clarence Yu, Chou, Fang-Chieh, Kladwang, Wipapat, Tian, Siqi, Cordero, Pablo, Das, Rhiju
Format: Article
Language:English
Subjects:
Accuracy
Adenosylcobalamin
Aptamers
Biochemistry
Biophysics and Structural Biology
Experiments
Gene expression
Glycine
high-throughput
Humans
Internal ribosome entry site
Ligands
Mapping
Models, Molecular
next-generation sequencing
Non-coding RNA
Nucleic Acid Conformation
Nucleotides
Protein structure
Puzzles
riboswitch
ribozyme
RNA Folding
RNA, Untranslated - chemistry
RNA, Untranslated - metabolism
Secondary structure
Spectrum analysis
structure prediction
Structure-function relationships
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Summary:Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.07600