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
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475
Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature · doi:10.1038/nature03441 · Cited by 1,872
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
Cited by
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
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
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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- The paper
- Verma, A., Halder, K., Halder, R., Yadav, V. K., Rawal, P., Thakur, R. K., Mohd, F., Sharma, A., & Chowdhury, S. (2008). Genome-Wide Computational and Expression Analyses Reveal G-Quadruplex DNA Motifs as Conserved cis-Regulatory Elements in Human and Related Species. Journal of Medicinal Chemistry. https://doi.org/10.1021/jm800448a
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