Prevalence of quadruplexes in the human genome.
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.
Huppert
Julian L
JL
University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK.
Balasubramanian
Shankar
S
D000465:Algorithms; D004247:DNA / Q000032:analysis* / Q000737:chemistry; D032621:DNA Shuffling; D054856:G-Quadruplexes; D015894:Genome, Human; D006147:Guanine / Q000032:analysis* / Q000737:chemistry; D006801:Humans; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D006147:Guanine; D004247:DNA