Affiliation:
1. Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
2. Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
Abstract
Abstract
G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in humans and a few other species. Recently, predictions have been made with bacterial and archaeal genomes. Nevertheless, a global comparison of predicted G4s (pG4s) across and within the three living kingdoms has not been addressed. In this study, we aimed to predict G4s in genes and transcripts of all kingdoms of living organisms and investigated the differences in their distributions. The relation of the predictions with GC content was studied. It appears that GC content is not the only parameter impacting G4 predictions and abundance. The distribution of pG4 densities varies depending on the class of transcripts and the group of species. Indeed, we have observed that, in coding transcripts, there are more predicted G4s than expected for eukaryotes but not for archaea and bacteria, while in noncoding transcripts, there are as many or fewer predicted G4s in all species groups. We even noticed that some species with the same GC content presented different pG4 profiles. For instance, Leishmania major and Chlamydomonas reinhardtii both have 60% of GC content, but the former has a pG4 density of 0.07 and the latter 1.16.
Funder
Canada Research Chairs
Chaire de recherche de l’Universite de Sherbrooke en Structure et Genomique de l’ARN
Fonds de recherche du Quebec - Nature et technologies
Natural Sciences and Engineering Research Council of Canada
Centre de Recherche du CHUS
Universite de Sherbrooke
Publisher
Oxford University Press (OUP)
Cited by
9 articles.
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