DNA:RNA hybrid G-quadruplex formation upstream of transcription start site.

Tytuł:: DNA:RNA hybrid G-quadruplex formation upstream of transcription start site.
Autorzy:: Zhang JY; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China.; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, P. R. China.
Xia Y; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China.
Hao YH; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China.
Tan Z; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China. .; Center for Healthy Aging, Changzhi Medical College, Changzhi, 046000, Shanxi, P. R. China. .
Źródło:: Scientific reports [Sci Rep] 2020 May 04; Vol. 10 (1), pp. 7429. Date of Electronic Publication: 2020 May 04.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: London : Nature Publishing Group, copyright 2011-
MeSH Terms:: G-Quadruplexes*
Transcription Initiation Site*
Guanine/*chemistry
Base Sequence ; Computational Biology ; DNA/genetics ; DNA-Directed RNA Polymerases/genetics ; Humans ; Nucleic Acid Conformation ; Oligonucleotides/genetics ; RNA/genetics ; Transcription, Genetic
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Xiao, S., Zhang, J. Y., Zheng, K. W., Hao, Y. H. & Tan, Z. Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals. Nucleic Acids Res 41, 10379–10390, https://doi.org/10.1093/nar/gkt781 (2013). (PMID: 10.1093/nar/gkt781239990963905843)
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Zheng, K. W. et al. Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control. Nucleic Acids Res 41, 5533–5541, https://doi.org/10.1093/nar/gkt264 (2013). (PMID: 10.1093/nar/gkt264235852813664831)
Xiao, S. et al. Formation of DNA:RNA hybrid G-quadruplexes of two G-quartet layers in transcription: expansion of the prevalence and diversity of G-quadruplexes in genomes. Angew Chem Int Ed Engl 53, 13110–13114, https://doi.org/10.1002/anie.201407045 (2014). (PMID: 10.1002/anie.20140704525267250)
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Zheng, K. W. et al. Superhelicity Constrains a Localized and R-Loop-Dependent Formation of G-Quadruplexes at the Upstream Region of Transcription. ACS Chem Biol 12, 2609–2618, https://doi.org/10.1021/acschembio.7b00435 (2017). (PMID: 10.1021/acschembio.7b0043528846373)
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Substance Nomenclature:: 0 (Oligonucleotides)
5Z93L87A1R (Guanine)
63231-63-0 (RNA)
9007-49-2 (DNA)
EC 2.7.7.6 (DNA-Directed RNA Polymerases)
Entry Date(s):: Date Created: 20200506 Date Completed: 20210106 Latest Revision: 20210504
Update Code:: 20240105
PubMed Central ID:: PMC7198591
DOI:: 10.1038/s41598-020-64117-x
PMID:: 32366914
: Czasopismo naukowe

Pełny tekst

Bioinformatic analysis reveals an enrichment of putative DNA:RNA hybrid G-quadruplex-forming sequences (PHQS) on both sides of the transcription start sites (TSSs) in the genome of warm-blooded animals, suggesting a positive selection of PHQSs in evolution and functional role of DNA:RNA hybrid G-quadruplexes (HQs) in transcription. The formation of HQs downstream of TSS in transcribed DNA has been documented under in vitro conditions; however, it is still not known if such HQs can form at the upstream side of TSSs. In this study, we report that such HQs can form in transcription in DNA with two to three guanine tracts if RNA carrying the required number of G-tracts is supplied. We also show that the formation of such HQs is dependent on the negative supercoiling generated by RNA polymerases. These results suggest that HQs may also form at the upstream side of TSSs in vivo and play a role in transcription since the two requirements are satisfied in cells.

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