title: The folding of 5'-UTR human G-quadruplexes possessing a long central loop.
abstract: G-quadruplexes are widespread four-stranded structures that are adopted by G-rich regions of both DNA and RNA and are involved in essential biological processes such as mRNA translation. They are formed by the stacking of two or more G-quartets that are linked together by three loops. Although the maximal loop length is usually fixed to 7 nt in most G-quadruplex-predicting software, it has already been demonstrated that artificial DNA G-quadruplexes containing two distal loops that are limited to 1 nt each and a central loop up to 30 nt long are likely to form in vitro. This report demonstrates that such structures possessing a long central loop are actually found in the 5'-UTRs of human mRNAs. Firstly, 1453 potential G-quadruplex-forming sequences (PG4s) were identified through a bioinformatic survey that searched for sequences respecting the requirement for two 1-nt long distal loops and a long central loop of 2-90 nt in length. Secondly, in vitro in-line probing experiments confirmed and characterized the folding of eight candidates possessing central loops of 10-70 nt long. Finally, the biological effect of several G-quadruplexes with a long central loop on mRNA expression was studied in cellulo using a luciferase gene reporter assay. Clearly, the actual definition of G-quadruplex-forming sequences is too conservative and must be expanded to include the long central loop. This greatly expands the number of expected PG4s in the transcriptome. Consideration of these new candidates might aid in elucidating the potentially important biological implications of the G-quadruplex structure.
authors.affiliation: Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8.
authors.forename: Rachel
authors.initials: R
authors.lastname: Jodoin
authors.affiliation: Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8.
authors.forename: Lubos
authors.initials: L
authors.lastname: Bauer
authors.affiliation: Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Garant
authors.affiliation: Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8.
authors.forename: Abdelhamid
authors.initials: A
authors.lastname: Mahdi Laaref
authors.affiliation: Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8.
authors.forename: Francis
authors.initials: F
authors.lastname: Phaneuf
authors.affiliation: Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Perreault
mesh_terms: D020121:5' Untranslated Regions; D001483:Base Sequence; D018797:Cell Cycle Proteins / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D054856:G-Quadruplexes; D056488:Histone Chaperones / Q000235:genetics; D006801:Humans; D000074008:MDS1 and EVI1 Complex Locus Protein; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D011519:Proto-Oncogenes / Q000235:genetics; D059370:RNA Folding; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; C091732:BCL2-associated athanogene 1 protein; D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; C086057:HIRA protein, human; D056488:Histone Chaperones; D000074008:MDS1 and EVI1 Complex Locus Protein; C063575:MECOM protein, human; D012333:RNA, Messenger; D014157:Transcription Factors
keywords: 5′-UTR; G-quadruplex; RNA structure; in-line probing; translation regulation