Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals. Xiao, S., Zhang, J., Zheng, K., Hao, Y., & Tan, Z. Nucleic acids research, 41(22):10379–90, December, 2013.
Paper doi abstract bibtex Recently, we reported the co-transcriptional formation of DNA:RNA hybrid G-quadruplex (HQ) structure by the non-template DNA strand and nascent RNA transcript, which in turn modulates transcription under both in vitro and in vivo conditions. Here we present bioinformatic analysis on putative HQ-forming sequences (PHQS) in the genomes of eukaryotic organisms. Starting from amphibian, PHQS motifs are concentrated in the immediate 1000-nt region downstream of transcription start sites, implying their potential role in transcription regulation. Moreover, their occurrence shows a strong bias toward the non-template versus the template strand. PHQS has become constitutional in genes in warm-blooded animals, and the magnitude of the strand bias correlates with the ability of PHQS to form HQ, suggesting a selection based on HQ formation. This strand bias is reversed in lower species, implying that the selection of PHQS/HQ depended on the living temperature of the organisms. In comparison with the putative intramolecular G-quadruplex-forming sequences (PQS), PHQS motifs are far more prevalent and abundant in the transcribed regions, making them the dominant candidates in the formation of G-quadruplexes in transcription. Collectively, these results suggest that the HQ structures are evolutionally selected to function in transcription and other transcription-mediated processes that involve guanine-rich non-template strand.
@article{Xiao2013,
title = {Bioinformatic analysis reveals an evolutional selection for {DNA}:{RNA} hybrid {G}-quadruplex structures as putative transcription regulatory elements in warm-blooded animals.},
volume = {41},
issn = {1362-4962},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23999096},
doi = {10.1093/nar/gkt781},
abstract = {Recently, we reported the co-transcriptional formation of DNA:RNA hybrid G-quadruplex (HQ) structure by the non-template DNA strand and nascent RNA transcript, which in turn modulates transcription under both in vitro and in vivo conditions. Here we present bioinformatic analysis on putative HQ-forming sequences (PHQS) in the genomes of eukaryotic organisms. Starting from amphibian, PHQS motifs are concentrated in the immediate 1000-nt region downstream of transcription start sites, implying their potential role in transcription regulation. Moreover, their occurrence shows a strong bias toward the non-template versus the template strand. PHQS has become constitutional in genes in warm-blooded animals, and the magnitude of the strand bias correlates with the ability of PHQS to form HQ, suggesting a selection based on HQ formation. This strand bias is reversed in lower species, implying that the selection of PHQS/HQ depended on the living temperature of the organisms. In comparison with the putative intramolecular G-quadruplex-forming sequences (PQS), PHQS motifs are far more prevalent and abundant in the transcribed regions, making them the dominant candidates in the formation of G-quadruplexes in transcription. Collectively, these results suggest that the HQ structures are evolutionally selected to function in transcription and other transcription-mediated processes that involve guanine-rich non-template strand.},
number = {22},
journal = {Nucleic acids research},
author = {Xiao, Shan and Zhang, Jia-Yu and Zheng, Ke-Wei and Hao, Yu-Hua and Tan, Zheng},
month = dec,
year = {2013},
pmid = {23999096},
keywords = {\#nosource},
pages = {10379--90},
}
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Here we present bioinformatic analysis on putative HQ-forming sequences (PHQS) in the genomes of eukaryotic organisms. Starting from amphibian, PHQS motifs are concentrated in the immediate 1000-nt region downstream of transcription start sites, implying their potential role in transcription regulation. Moreover, their occurrence shows a strong bias toward the non-template versus the template strand. PHQS has become constitutional in genes in warm-blooded animals, and the magnitude of the strand bias correlates with the ability of PHQS to form HQ, suggesting a selection based on HQ formation. This strand bias is reversed in lower species, implying that the selection of PHQS/HQ depended on the living temperature of the organisms. In comparison with the putative intramolecular G-quadruplex-forming sequences (PQS), PHQS motifs are far more prevalent and abundant in the transcribed regions, making them the dominant candidates in the formation of G-quadruplexes in transcription. Collectively, these results suggest that the HQ structures are evolutionally selected to function in transcription and other transcription-mediated processes that involve guanine-rich non-template strand.","number":"22","journal":"Nucleic acids research","author":[{"propositions":[],"lastnames":["Xiao"],"firstnames":["Shan"],"suffixes":[]},{"propositions":[],"lastnames":["Zhang"],"firstnames":["Jia-Yu"],"suffixes":[]},{"propositions":[],"lastnames":["Zheng"],"firstnames":["Ke-Wei"],"suffixes":[]},{"propositions":[],"lastnames":["Hao"],"firstnames":["Yu-Hua"],"suffixes":[]},{"propositions":[],"lastnames":["Tan"],"firstnames":["Zheng"],"suffixes":[]}],"month":"December","year":"2013","pmid":"23999096","keywords":"#nosource","pages":"10379–90","bibtex":"@article{Xiao2013,\n\ttitle = {Bioinformatic analysis reveals an evolutional selection for {DNA}:{RNA} hybrid {G}-quadruplex structures as putative transcription regulatory elements in warm-blooded animals.},\n\tvolume = {41},\n\tissn = {1362-4962},\n\turl = {http://www.ncbi.nlm.nih.gov/pubmed/23999096},\n\tdoi = {10.1093/nar/gkt781},\n\tabstract = {Recently, we reported the co-transcriptional formation of DNA:RNA hybrid G-quadruplex (HQ) structure by the non-template DNA strand and nascent RNA transcript, which in turn modulates transcription under both in vitro and in vivo conditions. 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