Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates

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dc.contributor.authorDvorak, Pavel
dc.contributor.authorLeupen, Sarah
dc.contributor.authorSoucek, Pavel
dc.date.accessioned2019-10-30T16:47:13Z
dc.date.available2019-10-30T16:47:13Z
dc.date.issued2019-06-21
dc.description.abstractSingle nucleotide polymorphisms located in 5' untranslated regions (50UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5' UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5' UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5' UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5' UTRs, such as GC content variation, hairpin structure conservation or 5' UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.en_US
dc.description.sponsorshipThis work was supported by the Czech Medical Council (project no. 17-28470A); National Sustainability Program I (project no. LO1503) and project no. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, both projects were awarded by the Ministry of Education, Youth and Sports of the Czech Republic and financed from The European Regional Development Fund; and Charles University Research Centre program UNCE/MED/006 “University Center of Clinical and Experimental Liver Surgery”.en_US
dc.description.urihttps://www.mdpi.com/2073-4409/8/6/623en_US
dc.format.extent24 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2kz9s-mwdf
dc.identifier.citationDvorak, P.; Leupen, S.; Soucek, P. Functionally Significant Features in the 5′ Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates. Cells 2019, 8, 623; https://doi.org/10.3390/cells8060623en_US
dc.identifier.urihttps://doi.org/10.3390/cells8060623
dc.identifier.urihttp://hdl.handle.net/11603/16006
dc.language.isoen_USen_US
dc.publisherMDPIen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Biological Sciences Department Collection
dc.relation.ispartofUMBC Faculty Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.
dc.rightsAttribution 4.0 International (CC BY 4.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.subject5' untranslated regionen_US
dc.subjectgene regulationen_US
dc.subjectsingle nucleotide polymorphismen_US
dc.subjectABCA1en_US
dc.subjectbioinformaticsen_US
dc.titleFunctionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebratesen_US
dc.typeTexten_US

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