ReviewHuman genetics2006
A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3' UTR variants.
Review in Human genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
63 citing papers in PubMed, 141 citations in OpenAlex.
- Association of innate immune single-nucleotide polymorphisms with the electroencephalogram during desflurane general anaesthesia.Journal of molecular neuroscience : MN · 2014Trial
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- Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-causing mechanism.American journal of human genetics · 2024Article
- NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin.Nucleic acids research · 2022Article
- Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures.PLoS computational biology · 2020Article
- A Hemizygous Deletion Within the PGK1 Gene in Males with PGK1 Deficiency.JIMD reports · 2019Article
- Antisense Oligonucleotide-Mediated Terminal Intron Retention of the SMN2 Transcript.Molecular therapy. Nucleic acids · 2018Article
- Resistin polymorphims, plasma resistin levels and obesity in Tunisian volunteers.Journal of clinical laboratory analysis · 2018Article
- Re-evaluating Strategies to Define the Immunoregulatory Roles of miRNAs.Trends in immunology · 2017Review
- Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns.RNA biology · 2016Article
- A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer.BMC medical genomics · 2016Article
- Genome-wide significant risk associations for mucinous ovarian carcinoma.Nature genetics · 2015Article
- Functional classification of 15 million SNPs detected from diverse chicken populations.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Association ofBiomedical reports · 2015Article
- The association between IGF-1 polymorphisms and high myopia.International journal of clinical and experimental medicine · 2015Article
- IL-17 gene polymorphism is associated with susceptibility to gastric cancer.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2014Article
- Allelic association, DNA resequencing and copy number variation at the metabotropic glutamate receptor GRM7 gene locus in bipolar disorder.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2014Article
- Post-transcriptional regulation of interferons and their signaling pathways.Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research · 2014Review
- The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes.BMC evolutionary biology · 2014Article
- Polymorphisms of ATF6B Are Potentially Associated With FEV1 Decline by Aspirin Provocation in Asthmatics.Allergy, asthma & immunology research · 2014Article
3 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
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In an attempt both to catalogue 3' regulatory region (3' RR)-mediated disease and to improve our understanding of the structure and function of the 3' RR, we have performed a systematic analysis of disease-associated variants in the 3' RRs of human protein-coding genes. We have previously analysed the variants that have occurred in two specific domains/motifs of the 3' untranslated region (3' UTR) as well as in the 3' flanking region. Here we have focused upon 83 known variants within the upstream sequence (USS; between the translational termination codon and the upstream core polyadenylation signal sequence) of the 3' UTR. To place these variants in their proper context, we first performed a comprehensive survey of known cis-regulatory elements within the USS and the mechanisms by which they effect post-transcriptional gene regulation. Although this survey supports the view that RNA regulatory elements function within the context of specific secondary structures, there are no general rules governing how secondary structure might exert its influence. We have therefore addressed this question by systematically evaluating both functional and non-functional (based upon in vitro reporter gene and/or electrophoretic mobility shift assay data) USS variant-containing sequences against known cis-regulatory motifs within the context of predicted RNA secondary structures. This has allowed us not only to establish a reliable and objective means to perform secondary structure prediction but also to identify consistent patterns of secondary structural change that could potentiate the discrimination of functional USS variants from their non-functional counterparts. The resulting rules were then used to infer potential functionality in the case of some of the remaining functionally uncharacterized USS variants, from their predicted secondary structures. This not only led us to identify further patterns of secondary structural change but also several potential novel cis-regulatory motifs within the 3' UTRs studied.
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What Socratic holds
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 Socratic graph.