IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-26312-w.html
   My bibliography  Save this article

Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing

Author

Listed:
  • Jing Tu

    (Southeast University)

  • Mengqin Duan

    (Southeast University)

  • Wenli Liu

    (Southeast University)

  • Na Lu

    (Southeast University)

  • Yue Zhou

    (Southeast University)

  • Xiao Sun

    (Southeast University)

  • Zuhong Lu

    (Southeast University)

Abstract

We present a user-friendly and transferable genome-wide DNA G-quadruplex (G4) profiling method that identifies G4 structures from ordinary whole-genome resequencing data by seizing the slight fluctuation of sequencing quality. In the human genome, 736,689 G4 structures were identified, of which 45.9% of all predicted canonical G4-forming sequences were characterized. Over 89% of the detected canonical G4s were also identified by combining polymerase stop assays with next-generation sequencing. Testing using public datasets of 6 species demonstrated that the present method is widely applicable. The detection rates of predicted canonical quadruplexes ranged from 32% to 58%. Because single nucleotide variations (SNVs) influence the formation of G4 structures and have individual differences, the given method is available to identify and characterize G4s genome-wide for specific individuals.

Suggested Citation

  • Jing Tu & Mengqin Duan & Wenli Liu & Na Lu & Yue Zhou & Xiao Sun & Zuhong Lu, 2021. "Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26312-w
    DOI: 10.1038/s41467-021-26312-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-26312-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-26312-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. David R. Bentley & Shankar Balasubramanian & Harold P. Swerdlow & Geoffrey P. Smith & John Milton & Clive G. Brown & Kevin P. Hall & Dirk J. Evers & Colin L. Barnes & Helen R. Bignell & Jonathan M. Bo, 2008. "Accurate whole human genome sequencing using reversible terminator chemistry," Nature, Nature, vol. 456(7218), pages 53-59, November.
    2. Aaron R. Haeusler & Christopher J. Donnelly & Goran Periz & Eric A. J. Simko & Patrick G. Shaw & Min-Sik Kim & Nicholas J. Maragakis & Juan C. Troncoso & Akhilesh Pandey & Rita Sattler & Jeffrey D. Ro, 2014. "C9orf72 nucleotide repeat structures initiate molecular cascades of disease," Nature, Nature, vol. 507(7491), pages 195-200, March.
    3. Andrew L. Wolfe & Kamini Singh & Yi Zhong & Philipp Drewe & Vinagolu K. Rajasekhar & Viraj R. Sanghvi & Konstantinos J. Mavrakis & Man Jiang & Justine E. Roderick & Joni Van der Meulen & Jonathan H. S, 2014. "RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer," Nature, Nature, vol. 513(7516), pages 65-70, September.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Kai-Bo Wang & Yushuang Liu & Jinzhu Li & Chengmei Xiao & Yingying Wang & Wei Gu & Yipu Li & Yuan-Zheng Xia & Tingdong Yan & Ming-Hua Yang & Ling-Yi Kong, 2022. "Structural insight into the bulge-containing KRAS oncogene promoter G-quadruplex bound to berberine and coptisine," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Geng Liu & Wenya Du & Xiongbo Sang & Qiyu Tong & Ye Wang & Guoqing Chen & Yi Yuan & Lili Jiang & Wei Cheng & Dan Liu & Yan Tian & Xianghui Fu, 2022. "RNA G-quadruplex in TMPRSS2 reduces SARS-CoV-2 infection," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Fiaz Ahmad Sulehri & Saba Sharif, 2022. "The Impact of Firm Sustainability on Firm Growth: Evidence from USA," Journal of Policy Research (JPR), Research Foundation for Humanity (RFH), vol. 8(2), pages 1-15, August.
    3. Ekaterina Borisova & Andrew G. Newman & Marta Couce Iglesias & Rike Dannenberg & Theres Schaub & Bo Qin & Alexandra Rusanova & Marisa Brockmann & Janina Koch & Marieatou Daniels & Paul Turko & Olaf Ja, 2024. "Protein translation rate determines neocortical neuron fate," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
    4. Xingxing Ren & Qiuyuan Liu & Peirong Zhou & Tingyue Zhou & Decai Wang & Qiao Mei & Richard A. Flavell & Zhanju Liu & Mingsong Li & Wen Pan & Shu Zhu, 2024. "DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Emily L. Spaulding & Alexis M. Feidler & Lio A. Cook & Dustin L. Updike, 2022. "RG/RGG repeats in the C. elegans homologs of Nucleolin and GAR1 contribute to sub-nucleolar phase separation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Mirjana Malnar Črnigoj & Urša Čerček & Xiaoke Yin & Manh Tin Ho & Barbka Repic Lampret & Manuela Neumann & Andreas Hermann & Guy Rouleau & Beat Suter & Manuel Mayr & Boris Rogelj, 2023. "Phenylalanine-tRNA aminoacylation is compromised by ALS/FTD-associated C9orf72 C4G2 repeat RNA," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Temitayo A. Olagunju & Benjamin D. Rosen & Holly L. Neibergs & Gabrielle M. Becker & Kimberly M. Davenport & Christine G. Elsik & Tracy S. Hadfield & Sergey Koren & Kristen L. Kuhn & Arang Rhie & Kati, 2024. "Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    8. Alla D. Fedorova & Stephen J. Kiniry & Dmitry E. Andreev & Jonathan M. Mudge & Pavel V. Baranov, 2022. "Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    9. Fajin Li & Jianhuo Fang & Yifan Yu & Sijia Hao & Qin Zou & Qinglin Zeng & Xuerui Yang, 2023. "Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    10. Hironori Saito & Yuma Handa & Mingming Chen & Tilman Schneider-Poetsch & Yuichi Shichino & Mari Takahashi & Daniel Romo & Minoru Yoshida & Alois Fürstner & Takuhiro Ito & Kaori Fukuzawa & Shintaro Iwa, 2024. "DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    11. Maja Olecka & Alena Bömmel & Lena Best & Madlen Haase & Silke Foerste & Konstantin Riege & Thomas Dost & Stefano Flor & Otto W. Witte & Sören Franzenburg & Marco Groth & Björn Eyss & Christoph Kaleta , 2024. "Nonlinear DNA methylation trajectories in aging male mice," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    12. Zhefan Stephen Chen & Mingxi Ou & Stephanie Taylor & Ruxandra Dafinca & Shaohong Isaac Peng & Kevin Talbot & Ho Yin Edwin Chan, 2023. "Mutant GGGGCC RNA prevents YY1 from binding to Fuzzy promoter which stimulates Wnt/β-catenin pathway in C9ALS/FTD," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    13. Amanda M. Gleixner & Brandie Morris Verdone & Charlton G. Otte & Eric N. Anderson & Nandini Ramesh & Olivia R. Shapiro & Jenna R. Gale & Jocelyn C. Mauna & Jacob R. Mann & Katie E. Copley & Elizabeth , 2022. "NUP62 localizes to ALS/FTLD pathological assemblies and contributes to TDP-43 insolubility," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    14. Tetsushi Sadakata & Yo Shinoda & Akira Sato & Hirotoshi Iguchi & Chiaki Ishii & Makoto Matsuo & Ryosuke Yamaga & Teiichi Furuichi, 2013. "Mouse Models of Mutations and Variations in Autism Spectrum Disorder-Associated Genes: Mice Expressing Caps2/Cadps2 Copy Number and Alternative Splicing Variants," IJERPH, MDPI, vol. 10(12), pages 1-19, November.
    15. Dasol Han & Guojing Liu & Yujeong Oh & Seyoun Oh & Seungbok Yang & Lori Mandjikian & Neha Rani & Maria C. Almeida & Kenneth S. Kosik & Jiwon Jang, 2023. "ZBTB12 is a molecular barrier to dedifferentiation in human pluripotent stem cells," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    16. Kazuki Ichikawa & Riki Kawahara & Takeshi Asano & Shinichi Morishita, 2023. "A landscape of complex tandem repeats within individual human genomes," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    17. Zheng Xu & Song Yan & Shuai Yuan & Cong Wu & Sixia Chen & Zifang Guo & Yun Li, 2023. "Efficient Two-Stage Analysis for Complex Trait Association with Arbitrary Depth Sequencing Data," Stats, MDPI, vol. 6(1), pages 1-14, March.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26312-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.