Whole genome experimental maps of DNA G-quadruplexes in multiple species
File(s)
Author(s)
Type
Journal Article
Abstract
Genomic maps of DNA G-quadruplexes (G4s) can help elucidate the roles that these secondary structures play in various organisms. Herein, we employ an improved version of a G-quadruplex sequencing method (G4-seq) to generate whole genome G4 maps for 12 species that include widely studied model organisms and also pathogens of clinical relevance. We identify G4 structures that form under physiological K+ conditions and also G4s that are stabilized by the G4-targeting small molecule pyridostatin (PDS). We discuss the various structural features of the experimentally observed G-quadruplexes (OQs), highlighting differences in their prevalence and enrichment across species. Our study describes diversity in sequence composition and genomic location for the OQs in the different species and reveals that the enrichment of OQs in gene promoters is particular to mammals such as mouse and human, among the species studied. The multi-species maps have been made publicly available as a resource to the research community. The maps can serve as blueprints for biological experiments in those model organisms, where G4 structures may play a role.
Date Issued
2019-05-07
Date Acceptance
2019-03-08
Citation
Nucleic Acids Research, 2019, 47 (8), pp.3862-3874
ISSN
0305-1048
Publisher
Oxford University Press
Start Page
3862
End Page
3874
Journal / Book Title
Nucleic Acids Research
Volume
47
Issue
8
Copyright Statement
©The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), whichpermits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/30892612
PII: 5403498
Subjects
Aminoquinolines
Animals
Arabidopsis
Base Sequence
Caenorhabditis elegans
Chromosome Mapping
Drosophila melanogaster
Escherichia coli
G-Quadruplexes
Genome
High-Throughput Nucleotide Sequencing
Humans
Leishmania major
Mice
Phylogeny
Picolinic Acids
Plasmodium falciparum
Rhodobacter sphaeroides
Saccharomyces cerevisiae
Trypanosoma brucei brucei
Zebrafish
Publication Status
Published
Coverage Spatial
England
Date Publish Online
2019-03-20