ArticleNucleic acids research2013
Widespread purifying selection on RNA structure in mammals.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
102 citing papers in PubMed, 177 citations in OpenAlex.
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- The emerging roles of long non-coding RNAs in the nervous system.Nature reviews. Neuroscience · 2025Review
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- SMDesigner: a program to design sequence mutations to assess RNA structure.RNA (New York, N.Y.) · 2025Article
- Massively parallel dissection of RNA in RNA-protein interactions in vivo.Nucleic acids research · 2024Article
- Hidden regulators: the emerging roles of lncRNAs in brain development and disease.Frontiers in neuroscience · 2024Review
- LncSTPred: a predictive model of lncRNA subcellular localization and decipherment of the biological determinants influencing localization.Frontiers in molecular biosciences · 2024Article
- Functional evolutionary convergence of long noncoding RNAs involved in embryonic development.Communications biology · 2023Article
- G-quadruplexes from non-coding RNAs.Journal of molecular medicine (Berlin, Germany) · 2023Review
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- Evolutionary Conservation of RNA Secondary Structure.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Controlling the uncontrolled variation in the diet induced obese mouse by microbiomic characterization.Scientific reports · 2022Article
- Genomic and functional conservation of lncRNAs: lessons from flies.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences.Genomics, proteomics & bioinformatics · 2022Article
- Evolutionary divergence ofRNA (New York, N.Y.) · 2022Article
- Does rapid sequence divergence preclude RNA structure conservation in vertebrates?Nucleic acids research · 2022Article
- Circulating MicroRNAs as Cancer Biomarkers in Liquid Biopsies.Advances in experimental medicine and biology · 2022Review
- SINEUPs: a novel toolbox for RNA therapeutics.Essays in biochemistry · 2021Review
- Comparative genomics in the search for conserved long noncoding RNAs.Essays in biochemistry · 2021Article
42 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies >4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5-22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1. This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.