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G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-hairpin-duplex switch

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Item Type:Article
Title:G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-hairpin-duplex switch
Creators Name:Kaplan, O.I. and Berber, B. and Hekim, N. and Doluca, O.
Abstract:Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns.
Keywords:Bacterial DNA, Bacterial Genome, Consensus Sequence, Escherichia coli, G-Quadruplexes, Gene Ontology, Inverted Repeat Sequences, Nucleic Acid Conformation, Nucleotide Motifs, Phylogeny, Position-Specific Scoring Matrices
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press (U.K.)
Volume:44
Number:19
Page Range:9083-9095
Date:2 November 2016
Official Publication:https://doi.org/10.1093/nar/gkw769
PubMed:View item in PubMed
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http://edoc.mdc-berlin.de/16875/Preprint version

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