Prevalence of quadruplexes in the human genome

By Julian Leon Huppert, Shankar Balasubramanian. Nucleic Acids Research, 2005

1,623 citations recorded by the source corpus.

Guanine-rich DNA sequences of a particular form have the ability to fold into four-stranded structures called G-quadruplexes. In this paper, we present a working rule to predict which primary sequences can form this structure, and describe a search algorithm to identify such sequences in genomic DNA. We count the number of quadruplexes found in the human genome and compare that with the figure predicted by modelling DNA as a Bernoulli stream or as a Markov chain, using windows of various sizes. We demonstrate that the distribution of loop lengths is significantly different from what would be expected in a random case, providing an indication of the number of potentially relevant quadruplex-forming sequences. In particular, we show that there is a significant repression of quadruplexes in the coding strand of exonic regions, which suggests that quadruplex-forming patterns are disfavoured in sequences that will form RNA.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/98c1cfdb6c5a4058211d690824437bb10b717738

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Citations in the corpus

Stability and kinetics of G-quadruplex structures (2008, background): “Such sequences are found in telomeres, and at a surprisingly high frequency in other parts of the genome, especially in promoters (1,2).”
G-quadruplexes and their regulatory roles in biology (2015, background): “Computational analyses of the human genome searching with the consensus sequence (G 3+ N 1–7 G 3+ N 1–7 G 3+ N 1–7 G 3+ ) revealed that it contains over 300 000 sequences that have the potential to form G-quadruplexes (pG4 or PQS) (12).”
Small molecule-induced DNA damage identifies alternative DNA structures in human genes (2012, neutral): “G-quadruplex nucleic acids may provide structural variations in the genom”
Quadruplex DNA: sequence, topology and structure (2006, background): “There have been two recent systematic surveys of the complete human genome sequence, searching for potential unimolecular quadruplex-forming sequences (18,19).”
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences (2006, background): “Although, G-quadruplexes have been surveyed in the human genome with such techniques (34,35), there are no known user-friendly computational tools easily accessible to the public.”
Highly prevalent putative quadruplex sequence motifs in human DNA (2005, methodology): “This agrees remarkably well with the estimate of 376 000 by a distinct approach (17).”
Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? (2011, background): “The advancement in our understanding of the biophysical principles that link G-quadruplex formation in vitro with oligonucleotide sequences has provided a rational basis for constructing algorithms that predict sequences that are likely to fold into intramolecular G-quadruplexe”
Circular dichroism and conformational polymorphism of DNA (2009, background): “Particular genomic regions, especially in gene promoters, have a potential to form quadruplexes (82,83), which are believed to form in vivo and affect cellular processes (79).”
The Structure and Function of DNA G-Quadruplexes (2020, methodology): “Based on biophysical studies on different G4 structures, algorithms using sequence motifs such as GR3NxGR3NxGR3NxGR3 were developed and deployed to predict putative G4 structures in genomic DNA [14,15].”
G-quadruplexes in promoters throughout the human genome (2006, methodology): “We have previously mapped out putative quadruplex sequences (PQS) in the human genome by a computational methodology, which identifies motifs of the form G3+N1 7 G3+N1 7G3+N1 7G3+ that we have shown are predisposed to the formation of intramolecular quadruplexes (9).”
Recent advances in RNA structurome (2022, background): “Canonical G4 structures can be bioinformatically predicted based on primary sequences (Figure 2B) (Huppert and Balasubramanian, 2005) and categorized into intra- and inter-mo-”