pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R

Hon, Jiří; Martínek, Tomáš; Zendulka, Jaroslav; Lexa, Matej

doi:10.1093/bioinformatics/btx413

Cited by 148 publications

(125 citation statements)

References 29 publications

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“…The motifs were found to be enriched in regulatory regions, especially promoters, first introns, and telomeres . Subsequent studies have led to the broadening of the G4‐motif definition and to the ongoing refinement of G4‐mining algorithms . However, major G4‐prone genomic fragments, including telomeres and oncogene promoters, are well established and the bioinformatics predictions are generally consistent with those from the G4‐sequencing data .…”

Section: Introductionmentioning

confidence: 94%

“…[18,19] Subsequent studies have led to the broadening of the G4-motif definition [20][21][22] and to the ongoing refinement of G4-mining algorithms. [23][24][25][26] However, major G4-prone genomic fragments, including telomeres and oncogene promoters, are well established and the bioinformatics predictions are generally consistent with those from the G4-sequencing data. [27] In living human cells, G4 foci have been found both inside and outside of telomeres using G4-specific antibodies.…”

Section: Introductionmentioning

confidence: 96%

See 1 more Smart Citation

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

2019

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Here, the emerging data on DNA G‐quadruplexes (G4s) as epigenetic modulators are reviewed and integrated. This concept has appeared and evolved substantially in recent years. First, persistent G4s (e.g., those stabilized by exogenous ligands) were linked to the loss of the histone code. More recently, transient G4s (i.e., those formed upon replication or transcription and unfolded rapidly by helicases) were implicated in CpG island methylation maintenance and de novo CpG methylation control. The most recent data indicate that there are direct interactions between G4s and chromatin remodeling factors. Finally, multiple findings support the indirect participation of G4s in chromatin reshaping via interactions with remodeling‐related transcription factors (TFs) or damage responders. Here, the links between the above processes are analyzed; also, how further elucidation of these processes may stimulate the progress of epigenetic therapy is discussed, and the remaining open questions are highlighted.

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Section: Introductionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 96%

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

2019

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“…We implemented the regular expression in python, returning a boolean expression dependent on the presence of a match in the presented sequence. The remaining three methods that were developed for the scoring of G4 forming potential are G4Hunter (Bedrat, Lacroix, and Mergny 2016) , Quadron (Sahakyan et al 2017) and Pqsfinder (Hon et al 2017) . We re-implemented G4Hunter in python as the available code did not appear functional (code available at our repository).…”

Section: Evaluation Schemementioning

confidence: 99%

“…A second wave of computational methods attempted to predict G4 locations after the publication of this dataset. Among the most accurate and still functional methods are G4Hunter (Bedrat, Lacroix, and Mergny 2016) , which expands the regular expression methods by scoring on G enrichment, Pqsfinder, which focuses on allowing customization for non-canonical G4s and was trained on the G4-Seq dataset (Hon et al 2017) , as well as Quadron (Sahakyan et al 2017) , a Machine Learning method trained on the G4-Seq dataset, utilizing the tree based Gradient Boosting Machine approach.…”

Section: Introductionmentioning

confidence: 99%

PENGUINN: Precise Exploration of Nuclear G-quadruplexes Using Interpretable Neural Networks

Klimentová

Poláček

Šimeček

et al. 2020

Preprint

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G-quadruplexes (G4s) are a class of stable structural nucleic acid motifs that are known to play a role in a wide spectrum of genomic functions, such as DNA replication and transcription. The classical understanding of G4 structure points to four variable length guanine strands joined by variable length stretches of other nucleotides. Experiments using G4 immunoprecipitation and sequencing experiments have produced a high number of highly probable G4 forming genomic sequences. The expense and technical difficulty of experimental techniques highlights the need for computational approaches of G4 identification. Here, we present PENGUINN, a machine learning method based on Convolutional Neural Networks, that learns the characteristics of G4 sequences and accurately predicts G4s outperforming the state-of-the-art. We provide both a standalone implementation of the trained model, and a web application that can be used to evaluate sequences for their G4 potential.

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“…For our prediction, we used G-tracts -3 or 4 and loop length 1-20 nucleotide [63]. The results were further cross verified by using QGRS Mapper [64] and PGSFinder [65] tools.…”

Section: G {T1} [X] {L1} G {T1} [X] {L2} G {T1} [X] {L3} G {T1}mentioning

confidence: 99%

G-quadruplex stabilization in the ions and maltose transporters inhibitSalmonella entericagrowth and virulence

Jain

Mishra

Shankar

et al. 2018

Preprint

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The G-quadruplex structure forming motifs have recently emerged as a novel therapeutic drug target in various human pathogens. Herein, we report three highly conserved G-quadruplex motifs (SE-PGQ-1, 2, and3) in genome of all the 412 strains of Salmonella enterica. Bioinformatics analysis inferred the presence of SE-PGQ-1 in the regulatory region of mgtA, presence of SE-PGQ-2 in the open reading frame of entA and presence of SE-PGQ-3 in the promoter region of malE and malK genes. The products of mgtA and entA are involved in transport and homeostasis of Mg 2+ and Fe 3+ ion and thereby required for bacterial survival in the presence of reactive nitrogen/oxygen species produced by the host macrophages, whereas, malK and malE genes are involved in transport of maltose sugar, that is one of the major carbon source in the gastrointestinal tract of human. The formation of stable intramolecular G-quadruplex structures by SE-PGQs was confirmed by employing CD, EMSA and NMR spectroscopy. Cellular studies revealed the inhibitory effect of 9-amino acridine on Salmonella enterica growth. Next, CD melting analysis demonstrated the stabilizing effect of 9-amino acridine on SE-PGQs. Further, polymerase inhibition and RT-qPCR assays emphasize the biological relevance of predicted G-quadruplex in the expression of PGQ possessing genes and demonstrate the G-quadruplexes as a potential drug target for the devolping novel therapeutics for combating Salmonella enterica infection.

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pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 148 publications

References 29 publications

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

PENGUINN: Precise Exploration of Nuclear G-quadruplexes Using Interpretable Neural Networks

G-quadruplex stabilization in the ions and maltose transporters inhibitSalmonella entericagrowth and virulence

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