Whole genome experimental maps of DNA G-quadruplexes in multiple species.
Chambers, Vicki S
Boutell, Jonathan M
Antonio, Marco Di
Nucleic acids research
Oxford University Press
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Marsico, G., Chambers, V. S., Sahakyan, A., McCauley, P., Boutell, J. M., Antonio, M. D., & Balasubramanian, S. (2019). Whole genome experimental maps of DNA G-quadruplexes in multiple species.. Nucleic acids research, 47 (8), 3862-3874. https://doi.org/10.1093/nar/gkz179
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.
Animals, Zebrafish, Humans, Mice, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Leishmania major, Trypanosoma brucei brucei, Escherichia coli, Rhodobacter sphaeroides, Saccharomyces cerevisiae, Arabidopsis, Picolinic Acids, Aminoquinolines, Chromosome Mapping, Phylogeny, Base Sequence, Genome, G-Quadruplexes, High-Throughput Nucleotide Sequencing
The S.B. research group is supported by programme grant funding from Cancer Research UK (C9681/A18618), European Research Council Advanced Grant No. 339778, a Wellcome Trust Senior Investigator Award (grant 209441/z/17/z) and by core funding from Cancer Research UK (C14303/A17197). We are grateful to the Biotechnology and Biological Sciences Research Council (BBSRC) and Illumina for the CASE studentship supporting V.S.C. (BB/I015477/1).
Cancer Research UK (18618)
Cancer Research UK (CB4330)
European Research Council (339778)
Wellcome Trust (209441/Z/17/Z)
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External DOI: https://doi.org/10.1093/nar/gkz179
This record's URL: https://www.repository.cam.ac.uk/handle/1810/290402