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...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research 2005-01, Vol.33 (9), p.2908-2916
Main Authors: Huppert, Julian L., Balasubramanian, Shankar
Format: Article
Language:English
Subjects:
Algorithms
DNA - analysis
DNA - chemistry
DNA Shuffling
G-Quadruplexes
Genome, Human
Guanine - analysis
Guanine - chemistry
Humans
Nucleic Acid Conformation
Sequence Analysis, DNA - methods
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gki609