ArticleBMC bioinformatics2016
Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 33 citations in OpenAlex.
- RNA Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Parental noncoding RNA expression dynamics across sperm, oocyte, and zygote.NAR genomics and bioinformatics · 2025Article
- mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts.RNA biology · 2024Review
- DeepRaccess: high-speed RNA accessibility prediction using deep learning.Frontiers in bioinformatics · 2023Article
- RNA Secondary Structure Alteration Caused by Single Nucleotide Variants.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Genome-Wide RNA Secondary Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation.Nucleic acids research · 2022Article
- A protocol to construct RNA-protein devices for photochemical translational regulation of synthetic mRNAs in mammalian cells.STAR protocols · 2022Article
- LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods.Bioinformatics advances · 2022Article
- RNA structure-wide discovery of functional interactions with multiplexed RNA motif library.Nature communications · 2020Article
- RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp.BMC bioinformatics · 2020Article
- Caliciviral protein-based artificial translational activator for mammalian gene circuits with RNA-only delivery.Nature communications · 2020Article
- reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction.BMC bioinformatics · 2019Article
- Identifying sequence features that drive ribosomal association for lncRNA.BMC genomics · 2018Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.Bioinformatics (Oxford, England) · 2017Article
- Comparative analysis of lincRNA in insect species.BMC evolutionary biology · 2017Article
- Function by Structure: Spotlights on Xist Long Non-coding RNA.Frontiers in molecular biosciences · 2017Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems.
resultsOur novel software, "ParasoR", is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions.
conclusionsWe have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a million bases in the human genome. In our analyses, transcribed regions including introns are indicated to be subject to various types of structural constraints that cannot be explained from simple sequence composition biases. ParasoR is freely available at https://github.com/carushi/ParasoR .
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