G-quadruplex prediction inE. coligenome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

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.

Case studies on potential G-quadruplex-forming sequences from the bacterial orders Deinococcales and Thermales derived from a survey of published genomes

“…coli , yeast, and A . thaliana were previously reported 41 , 46 . The genomes of tardigrade (a.k.a., water bear) and rice have similar PQS densities as found in the large genome cluster (300 PQSs/Mbp).…”

“…The G-rich sequences were found to be biased toward gene promoters, 5′-UTRs, and the first intron, in addition to repeat sequences such as the telomere. This type of analysis now has been extended to select plant and microorganism genomes 41 – 47 , in addition to the DNA or RNA genomes found in viruses 48 – 53 . The massive implementation of more affordable next-generation DNA sequencing has enabled sequencing of thousands of genomes, particularly those from microorganisms.…”

G-Quadruplex enrichment analysis reveals their role as intronic regulatory elements in plants

“…These G-quadruplexes may share similarity in topology, which requires biophysical experimentation. Alternatively, the similarities of these G-quadruplexes may be captured through pairwise comparison of the sequences that form the G-quadruplex as we have suggested previously (Kaplan et al, 2016). Each G-quadruplex-forming sequence in a hotspot or a negative control was compared using pairwise alignment using the biopython package with local alignment function and a match score of 1 and mismatch, gap opening, and gap extension penalties of -2, -4, and -0.5, respectively.…”

“…One type might have stronger interaction with a particular transcription factor and thus result in a stronger coregulation. We previously suggested that G4 topology would have different effects at the molecular level and suggested clustering based on topological similarities (Kaplan et al, 2016). Topologies of the G4s, of course, cannot be identified accurately without extensive analysis of every single G4 computationally predicted in a genome and even that is prone to deformation in vivo.…”

A Thioflavin T-induced G-Quadruplex Fluorescent Biosensor for Target DNA Detection

“…15 In recent years, its property and applications have become a research hotspot. [16][17][18][19] A lot of colorimetric methods and electrochemical strategies have employed G-quadruplex systems for target detection because of the formation of a G-quadruplex/hemin complex, which is a horseradish peroxidase (HRP) mimicking DNAzyme. 9,20,21 Meanwhile, the G-quadruplex has also been widely applied in fluorescent biosensors [22][23][24] because it can specifically combine with some fluorescent dyes, causing significantly higher fluorescence intensities than those of dyes alone.…”