Cited by 570RNA and protein synthesis mechanismsRNA Research and SplicingRNA regulation and disease

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Landscape and variation of RNA secondary structure across the human transcriptome

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Wan, Yue, Qu, Kun, Zhang, Qiangfeng Cliff, Flynn, Ryan A., Manor, Ohad, Ouyang, Zhengqing, Zhang, Jiajing, Spitale, Robert C., Snyder, Michael P., Segal, Eran, Chang, Howard Y.·2014·Nature

DOI 10.1038/nature12946PMC PMC3973747

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Abstract

In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comprehensive RSS map of human coding and non-coding RNAs. We identify unique RSS signatures that demarcate open reading frames and splicing junctions, and define authentic microRNA-binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1,900 transcribed single nucleotide variants (approximately 15% of all transcribed single nucleotide variants) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSSs. Selective depletion of 'riboSNitches' versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3' untranslated regions, binding sites of microRNAs and RNA-binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.

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Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
MicroRNAs: Target Recognition and Regulatory Functions
Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068
Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets
Lewis, B. P., Burge, C. B., & Bartel, D. P. (2005) · Cell · doi:10.1016/j.cell.2004.12.035 · Cited by 11,855
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Self-citation
MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
Grimson, A., Farh, K. K.-H., Johnston, W. K., Garrett-Engele, P., Lim, L. P., & Bartel, D. P. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.017 · Cited by 3,766
Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps
Chi, S. W., Zang, J. B., Mele, A., & Darnell, R. B. (2009) · Nature · doi:10.1038/nature08170 · Cited by 1,791
Analysis and design of RNA sequencing experiments for identifying isoform regulation
Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. (2010) · Nature Methods · doi:10.1038/nmeth.1528 · Cited by 1,353
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1838 · Cited by 1,126
The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
Barbosa-Morais, N. L., Irimia, M., Pan, Q., Xiong, H. Y., Gueroussov, S., Lee, L. J., Slobodeniuc, V., Kutter, C., Watt, S., Çolak, R., et al. (2012) · Science · doi:10.1126/science.1230612 · Cited by 1,063

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Wang, Y., Zhu, X., Sun, M., Chen, Y., Chen, Y., Tu, S., Bai, B., Chen, M., Dai, Q., Wang, H., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/043232 · Cited by 1
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Iwakiri, J., & Asai, K. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20286-0 · Cited by 1
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Yu, M., Guo, W., Wang, Q., & Chen, J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/685016 · Cited by 1
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An Enterovirus-Like RNA Construct for Colon Cancer Suicide Gene Therapy.
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Burbridge, J. (2015) · Journal of International Crisis and Risk Communication Research
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Betts, J. A. (2016) · The University of Queensland · doi:10.14264/uql.2016.158
Loss of Sbds in Shwachman-Diamond Syndrome Murine Model Leads to Reduction of 80S Ribosomes and Altered Transcript Binding
Liu, H. (2016) · TSpace (University of Toronto)
GIC: A computational method for predicting the essentiality of long noncoding lncRNAsPreprint
Zeng, P., Chen, J., Zhou, Y., Yang, J., & Cui, Q. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/177923
IDENTIFICATION OF RNA STRUCTURES MODULATING THE EXPRESSION OF THE mRNA BIOGENESIS FACTOR SUS1
AbuQattam, A. (2017) · RiuNet (Universitat Politècnica de València) · doi:10.4995/thesis/10251/90524
Computational analysis of genomic variants affecting predicted microRNA:target interactions in prostate cancer.
Pérez, A. (2018) · doi:10.5642/kgitd/6
Insights into the structure-driven protein interactivity of RNA moleculesPreprint
de Groot, N. S., Armaos, A., Montes, R. G., Alriquet, M., Calloni, G., Vabulas, R. M., & Tartaglia, G. G. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/436279
An Integrative Study of Ribonucleoprotein Condensates Reveals a Biomarker for Fragile X-Associated Tremor/Ataxia SyndromePreprint
Botta‐Orfila, T., Cid-Samper, F., Gelabert‐Baldrich, M., Lang, B., Lorenzo-Gotor, N., Ponti, R. D., Severijnen, L.-A. W. F. M., Bolognesi, B., Gelpí, E., Hukema, R. K., et al. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3206267
Υπολογιστική ανάλυση των λειτουργιών των μη κωδικών μεταγραφών στη γονιδιωματική ρύθμιση
Karagkouni, D. (2019) · doi:10.12681/eadd/45135
The functional effects of RNA structure: from riboSNitches to translational control
Corley, M. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/y9db-eh66
Functional and structural basis of extreme non-coding conservation in vertebrate 5’UTRsPreprint
Byeon, G. W., Cenik, E. S., Jiang, L., Tang, H., Das, R., & Barna, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.29.165878
Logistic big data prediction of gastric cancer
Wang, Y., Zhong, C., & Zheng, Y. (2020) · Journal of Physics Conference Series · doi:10.1088/1742-6596/1650/3/032164
Genome-Wide Probing of RNA Structure
Huo, X., Ng, J., Tan, M., & Tucker‐Kellogg, G. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.20145-3
Mistranslation drives alterations in protein levels and the effects of a synonymous variant at the FGF21 locus
Bayoumi, A. (2020) · The Sydney eScholarship Repository (The University of Sydney)
Next-Generation Sequencing Techniques to Study HIV-1 Transcription and RNA Structure
Tomezsko, P. J. (2020) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
Cell-Free Synthetic Biosensors Based on CRISPR/Cas Mediated Cascade Signal Amplification for Precise RNA DetectionPreprint
Zhang, C., Zhang, P., Ren, H., Jia, P., Ji, J., Cao, L., Yang, P., Li, Y., Liu, J., Li, Z., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-358218/v1
Gene expression in sight
Sonneveld, S. (2021) · Utrecht University Repository (Utrecht University) · doi:10.33540/858
Exploring RNAs Interactions and Polymorphisms in the Pathophysiology of Pemphigus: A Review
Bahrami, A., Taheri, M. N., Habibi, P., Soleimani, M., & Nouri, F. (2021) · Avicenna Journal of Pharmaceutical Research · doi:10.34172/ajpr.2021.06

Authors: Wan, Y., Qu, K., Zhang, Q. C., Flynn, R. A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R. C., Snyder, M. P., Segal, E., & Chang, H. Y.
Affiliations: Howard Hughes Medical Institute (US)
Weizmann Institute of Science (IL)
Stanford Medicine (US)
Corresponding author: Wan, Yue
Chang, Howard Y.
ORCID: Wan, Yue
Qu, Kun
Zhang, Qiangfeng Cliff
Flynn, Ryan A.
Manor, Ohad
Ouyang, Zhengqing
Zhang, Jiajing
Spitale, Robert C.
Snyder, Michael P.
Segal, Eran
Chang, Howard Y.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2014-01-29
Volume: 505
Issue: 7485
Pages: 706-709
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature12946
PMC: PMC3973747
OpenAlex: W2071717527
Cited by: 555
References: 26
Citations by year: 2026: 29 · 2025: 24 · 2024: 26 · 2023: 30 · 2022: 40 · 2021: 50 · 2020: 52 · 2019: 37 · 2018: 61 · 2017: 40 · 2016: 56 · 2015: 71 · 2014: 39
FWCI: 28.31
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
eScholarship (California Digital Library) (submittedVersion, cc-by)
The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
Funders: Howard Hughes Medical Institute
National Human Genome Research Institute (R01HG004361)
National Cancer Institute (T32CA009302, P30CA034196)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords: RNA secondary structure, human transcriptome, single nucleotide variants, RNA structure prediction, gene expression regulation, single-stranded RNA, Arabidopsis thaliana, yeast, non-coding RNA, splice sites, polyadenylation
MeSH terms: Base Sequence, Binding Sites, Child, Female, Gene Expression Regulation, Humans, Male, Nucleic Acid Conformation, RNA, Genome, Human, Open Reading Frames, RNA-Binding Proteins, Point Mutation, 3' Untranslated Regions, RNA Splice Sites, MicroRNAs, Transcriptome

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