IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-45968-8.html
   My bibliography  Save this article

Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination

Author

Listed:
  • Gerardo Patiño-Guillén

    (University of Cambridge)

  • Jovan Pešović

    (Centre for Human Molecular Genetics)

  • Marko Panić

    (Centre for Human Molecular Genetics
    Vaccines and Sera “Torlak”)

  • Dušanka Savić-Pavićević

    (Centre for Human Molecular Genetics)

  • Filip Bošković

    (University of Cambridge)

  • Ulrich Felix Keyser

    (University of Cambridge)

Abstract

Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.

Suggested Citation

  • Gerardo Patiño-Guillén & Jovan Pešović & Marko Panić & Dušanka Savić-Pavićević & Filip Bošković & Ulrich Felix Keyser, 2024. "Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45968-8
    DOI: 10.1038/s41467-024-45968-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-45968-8
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-45968-8?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. Mihue Jang & Jong Hwan Kim & Hae Yun Nam & Ick Chan Kwon & Hyung Jun Ahn, 2015. "Design of a platform technology for systemic delivery of siRNA to tumours using rolling circle transcription," Nature Communications, Nature, vol. 6(1), pages 1-12, November.
    2. Ke Liu & Chao Pan & Alexandre Kuhn & Adrian Pascal Nievergelt & Georg E. Fantner & Olgica Milenkovic & Aleksandra Radenovic, 2019. "Detecting topological variations of DNA at single-molecule level," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    3. Felipe Rivas & Osama K. Zahid & Heidi L. Reesink & Bridgette T. Peal & Alan J. Nixon & Paul L. DeAngelis & Aleksander Skardal & Elaheh Rahbar & Adam R. Hall, 2018. "Label-free analysis of physiological hyaluronan size distribution with a solid-state nanopore sensor," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    4. Rajesh Kumar Sharma & Ishita Agrawal & Liang Dai & Patrick S. Doyle & Slaven Garaj, 2019. "Complex DNA knots detected with a nanopore sensor," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    Full references (including those not matched with items on IDEAS)

    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. Parisa Bayat & Charlotte Rambaud & Bernard Priem & Matthieu Bourderioux & Mélanie Bilong & Salomé Poyer & Manuela Pastoriza-Gallego & Abdelghani Oukhaled & Jérôme Mathé & Régis Daniel, 2022. "Comprehensive structural assignment of glycosaminoglycan oligo- and polysaccharides by protein nanopore," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Minmin Li & Yuting Xiong & Yuchen Cao & Chen Zhang & Yuting Li & Hanwen Ning & Fan Liu & Han Zhou & Xiaonong Li & Xianlong Ye & Yue Pang & Jiaming Zhang & Xinmiao Liang & Guangyan Qing, 2023. "Identification of tagged glycans with a protein nanopore," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Lauren S. Lastra & Y. M. Nuwan D. Y. Bandara & Michelle Nguyen & Nasim Farajpour & Kevin J. Freedman, 2022. "On the origins of conductive pulse sensing inside a nanopore," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Ling-Jun Kong & Weixuan Zhang & Peng Li & Xuyue Guo & Jingfeng Zhang & Furong Zhang & Jianlin Zhao & Xiangdong Zhang, 2022. "High capacity topological coding based on nested vortex knots and links," Nature Communications, Nature, vol. 13(1), pages 1-8, December.

    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:15:y:2024:i:1:d:10.1038_s41467-024-45968-8. 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.