ArticleBMC genomics2008
Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed, 16 citations in OpenAlex.
- 3'READS + RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association.RNA (New York, N.Y.) · 2020Article
- NoFold: RNA structure clustering without folding or alignment.RNA (New York, N.Y.) · 2014Article
- Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.Nucleic acids research · 2012Article
- A method for discovering common patterns from two RNA secondary structures and its application to structural repeat detection.Journal of bioinformatics and computational biology · 2012Article
- Searching for non-coding RNAs in genomic sequences using ncRNAscout.Genomics, proteomics & bioinformatics · 2012Article
- New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.Genome research · 2011Article
- mRNA secondary structures fold sequentially but exchange rapidly in vivo.PLoS biology · 2010Article
- Properties of untranslated regions of the S. cerevisiae genome.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. Several RNA stem-loop structures in UTRs have been experimentally identified, including the histone 3' UTR stem-loop structure (HSL3) and iron response element (IRE). These stem-loop structures are conserved among mammalian orthologs, and exist in a group of genes encoding proteins involved in the same biological pathways. It is not known to what extent RNA structures like these exist in all mammalian UTRs.
resultsIn this paper we took a systematic approach, named GLEAN-UTR, to identify small stem-loop RNA structure elements in UTRs that are conserved between human and mouse orthologs and exist in multiple genes with common Gene Ontology terms. This approach resulted in 90 distinct RNA structure groups containing 748 structures, with HSL3 and IRE among the top hits based on conservation of structure.
conclusionOur result indicates that there may exist many conserved stem-loop structures in mammalian UTRs that are involved in coordinate post-transcriptional regulation of biological pathways.
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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.