ArticleNature communications2018
Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing.Nucleic acids research · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity.Nature structural & molecular biology · 2025Article
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
- In vivo secondary structural analysis of Influenza A virus genomic RNA.Cellular and molecular life sciences : CMLS · 2023Article
- Probing the dynamic RNA structurome and its functions.Nature reviews. Genetics · 2023Review
- Functional knockout of long non-coding RNAs with genome editing.Frontiers in genetics · 2023Review
- High-temperature adaptation of anScience advances · 2022Article
- Advances and opportunities in RNA structure experimental determination and computational modeling.Nature methods · 2022Review
- ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence.Nucleic acids research · 2022Article
- Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.Nature communications · 2022Article
- Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.RNA biology · 2021Article
- Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets.NAR genomics and bioinformatics · 2021Article
- Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.Molecular cell · 2021Article
- Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units.Computational and structural biotechnology journal · 2021Article
- Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP.Nature communications · 2020Article
- Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- Helix-Based RNA Landscape Partition and Alternative Secondary Structure Determination.ACS omega · 2019Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
RNA plays key regulatory roles in diverse cellular processes, where its functionality often derives from folding into and converting between structures. Many RNAs further rely on co-existence of alternative structures, which govern their response to cellular signals. However, characterizing heterogeneous landscapes is difficult, both experimentally and computationally. Recently, structure profiling experiments have emerged as powerful and affordable structure characterization methods, which improve computational structure prediction. To date, efforts have centered on predicting one optimal structure, with much less progress made on multiple-structure prediction. Here, we report a probabilistic modeling approach that predicts a parsimonious set of co-existing structures and estimates their abundances from structure profiling data. We demonstrate robust landscape reconstruction and quantitative insights into structural dynamics by analyzing numerous data sets. This work establishes a framework for data-directed characterization of structure landscapes to aid experimentalists in performing structure-function studies.
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