Skip to main content
SpringerLink
Log in

Effect of Promoter G-quadruplex on Gene Expression and Its Interaction with Transcription Factor

  • Conference paper
  • First Online:
12th Asian-Pacific Conference on Medical and Biological Engineering (APCMBE 2023)

Part of the book series: IFMBE Proceedings ((IFMBE,volume 103))

Included in the following conference series:

  • 130 Accesses

Abstract

G-quadruplexes (G4s) are special nucleic acid structures widely found in human genome. They are enriched in important regions such as telomeres and promoters and are involved in important biological processes including gene transcription and DNA replication. G4s are associated with many diseases. In this study, we use high-throughput sequencing data to analyze the distribution of G4s and their effects on gene expression and to explore the synergistic effects of G4s and transcription factors (TFs) on gene expression. The analysis of the interaction between G4 and TFs provides new insights into the biological functions of G4 and offers new opportunities for G4-based disease therapy.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Chambers, V.S., Marsico, G., Boutell, J.M., Di Antonio, M., et al.: High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 33, 877-+ (2015). https://doi.org/10.1038/nbt.3295

  2. Marsico, G., Chambers, V.S., Sahakyan, A.B., et al.: Whole genome experimental maps of DNA G-quadruplexes in multiple species. Nucleic Acids Res. 47, 3862–3874 (2019). https://doi.org/10.1093/nar/gkz179

    Article  Google Scholar 

  3. de Lange, T.: Shelterin: the protein complex that shapes and safeguards human telomeres. Genes Dev. 19, 2100–2110 (2005). https://doi.org/10.1101/gad.1346005

    Article  Google Scholar 

  4. Thakur, R.K., Kumar, P., Halder, K., et al.: Metastases suppressor NM23-H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression. Nucleic Acids Res. 37, 172–183 (2009). https://doi.org/10.1093/nar/gkn919

    Article  Google Scholar 

  5. Cogoi, S., Shchekotikhin, A.E., Xodo, L.E.: HRAS is silenced by two neighboring G-quadruplexes and activated by MAZ, a zinc-finger transcription factor with DNA unfolding property. Nucleic Acids Res. 42, 8379-U147 (2014). https://doi.org/10.1093/nar/gku574

    Article  Google Scholar 

  6. David, A.P., Pipier, A., Pascutti, F., et al.: CNBP controls transcription by unfolding DNA G-quadruplex structures. Nucleic Acids Res. 47, 7901–7913 (2019). https://doi.org/10.1093/nar/gkz527

    Article  Google Scholar 

  7. Kouzine, F., Wojtowicz, D., Baranello, L., et al.: Permanganate/S1 nuclease footprinting reveals Non-B DNA structures with regulatory potential across a mammalian genome. Cell Syst. 4, 344–356 (2017). https://doi.org/10.1016/j.cels.2017.01.013

    Article  Google Scholar 

  8. Hansel-Hertsch, R., Beraldi, D., Lensing, S.V., et al.: G-quadruplex structures mark human regulatory chromatin. Nat. Genet. 48(10), 1267–1272 (2016). https://doi.org/10.1038/ng.3662

    Article  Google Scholar 

  9. Spiegel, J., Cuesta, S.M., Adhikari, S., et al.: G-quadruplexes are transcription factor binding hubs in human chromatin. Genome Biol. 22, 117 (2021). https://doi.org/10.1186/s13059-021-02324-z

  10. Frankish, A., et al.: GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47, D766–D773 (2019). https://doi.org/10.1093/nar/gky955

    Article  Google Scholar 

  11. Hammal, F., de Langen, P., et al.: ReMap 2022: a database of human, mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res. 50, D316–D325 (2022). https://doi.org/10.1093/nar/gkab996

    Article  Google Scholar 

  12. Ghandi, M., et al.: Next-generation characterization of the cancer cell line encyclopedia. Nature 569, 503–508 (2019). https://doi.org/10.1038/s41586-019-1186-3

    Article  Google Scholar 

  13. Huang, W., Loganantharaj, R., Schroeder, B., et al.: PAVIS: a tool for peak annotation and visualization. Bioinformatics 29, 3097–3099 (2013). https://doi.org/10.1093/bioinformatics/btt520

    Article  Google Scholar 

  14. Shen, J., Varshney, D., Simeone, A., et al.: Promoter G-quadruplex folding precedes transcription and is controlled by chromatin. Genome Biol. 22, 143 (2021). https://doi.org/10.1186/s13059-021-02346-7

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biological Science and Medical Engineering, Southeast University, Nanjing, China

    Jiahuan Liu & Xiao Sun

Authors
  1. Jiahuan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiao Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiao Sun .

Editor information

Editors and Affiliations

  1. Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China

    Guangzhi Wang

  2. School of Life Science and Technology, University of Electronic Science and Technology, Chengdu, China

    Dezhong Yao

  3. State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China

    Zhongze Gu

  4. Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine Peking Union Medical College, Beijing, China

    Yi Peng

  5. School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China

    Shanbao Tong

  6. State Key Laboratory of Bioelectronics, School of Instrument Science and Engineering, Southeast University, Nanjing, China

    Chengyu Liu

Rights and permissions

Reprints and permissions

Copyright information

© 2024 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Liu, J., Sun, X. (2024). Effect of Promoter G-quadruplex on Gene Expression and Its Interaction with Transcription Factor. In: Wang, G., Yao, D., Gu, Z., Peng, Y., Tong, S., Liu, C. (eds) 12th Asian-Pacific Conference on Medical and Biological Engineering. APCMBE 2023. IFMBE Proceedings, vol 103. Springer, Cham. https://doi.org/10.1007/978-3-031-51455-5_7

Download citation

  • DOI: https://doi.org/10.1007/978-3-031-51455-5_7

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-51454-8

  • Online ISBN: 978-3-031-51455-5

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics

Search

Navigation