The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Genome-Wide Computational and Expression Analyses Reveal G-Quadruplex DNA Motifs as Conserved cis-Regulatory Elements in Human and Related Species
Abstract
Using a combination of in silico and experimental approaches, we present evidence that the G-quadruplex (G4) motif (an alternative higher-order DNA conformation) has regulatory potential. Genome-wide analyses of 99980 human, chimpanzee, mouse, and rat promoters showed enrichment of sequence with potential to adopt G4 (potential G4 or PG4) motifs near transcription start sites (TSS; P < 0.0001), supporting earlier findings. Interestingly, we found >700 orthologously related promoters in human, mouse, and rat conserve PG4 motif(s). The corresponding genes have enriched (z score > 4.0) tissue-specific expression in 75 of 79 human tissues and are significantly overrepresented in signaling and regulation of cell-cycle (P < 10(-05)). This is supported by results from whole genome expression experiments in human HeLa S3 cells following treatment with TMPyP4 [5,10,15,20-tetra(N-methyl-4-pyridyl) porphine chloride], which is known to bind the G4 motif inside cells. Our results implicate G4-motif mediated regulation as a more general mode of transcription control than currently appreciated.
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Cites
A gene atlas of the mouse and human protein-encoding transcriptomes
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An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation
Kumari, S., Bugaut, A., Huppert, J. L., & Balasubramanian, S. (2007) · Nature Chemical Biology · doi:10.1038/nchembio864 · Cited by 822
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G-quadruplex nucleic acids as therapeutic targets
Balasubramanian, S., & Neidle, S. (2009) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2009.04.637 · Cited by 586
Making sense of G‐quadruplex and i‐motif functions in oncogene promoters
Brooks, T. A., Kendrick, S., & Hurley, L. (2010) · The FEBS Journal · doi:10.1111/j.1742-4658.2010.07759.x · Cited by 477
G-quadruplex structures are stable and detectable in human genomic DNA
Lam, E. Y. N., Beraldi, D., Tannahill, D., & Balasubramanian, S. (2013) · Nature Communications · doi:10.1038/ncomms2792 · Cited by 455
RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms
Fay, M. M., Lyons, S. M., & Ivanov, P. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.05.017 · Cited by 447
The structures of quadruplex nucleic acids and their drug complexes
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Whole genome experimental maps of DNA G-quadruplexes in multiple species
Marsico, G., Chambers, V. S., Sahakyan, A. B., McCauley, P., Boutell, J. M., Antonio, M. D., & Balasubramanian, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz179 · Cited by 431
Targeting MYC Expression through G-Quadruplexes
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Brooks, T. A., & Hurley, L. H. (2009) · Nature Reviews Cancer · doi:10.1038/nrc2733 · Cited by 294
5′-UTR G-quadruplex structures acting as translational repressors
Beaudoin, J.-D., & Perreault, J.-P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq557 · Cited by 255
Elevated Levels of G-Quadruplex Formation in Human Stomach and Liver Cancer Tissues
Biffi, G., Tannahill, D., Miller, J., Howat, W. J., & Balasubramanian, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0102711 · Cited by 223
“The predicted location of G-quadruplex sequence motifs in regulatory regions of the genome, such as promoters and telomeres, suggests that Gquadruplex structures may have important roles in genome function [5–7].”
BackgroundG-quadruplex unwinding helicases and their function in vivo
Sauer, M., & Paeschke, K. (2017) · Biochemical Society Transactions · doi:10.1042/bst20170097 · Cited by 179
Metadata
- Authors
- Verma, A., Halder, K., Halder, R., Yadav, V. K., Rawal, P., Thakur, R. K., Mohd, F., Sharma, A., & Chowdhury, S.
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2008-09-04
- Volume
- 51
- Issue
- 18
- Pages
- 5641-5649
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- OpenAlex
- W2027696068
- Cited by
- 236
- References
- 3
- FWCI
- 5.83
- Type
- journal article
- Language
- en
- Open access
- closed
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