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 algo-rithm to identify such sequences in genomic DNA. We count thenumberofquadruplexes foundinthehuman 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 demon-strate that the distribution of loop lengths is signific-antly 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 cod-ing strand of exonic regions, which suggests that quadruplex-forming patterns are disfavoured in sequences that will form RNA