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Novel Insights of the Gene Translational Dynamic and Complex Revealed by Ribosome Profiling

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Systems Biology

Part of the book series: RNA Technologies ((RNATECHN))

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Abstract

Biology research has entered into the big data era. Systems biology approaches, therefore, have become essential tools to elucidate the whole landscape of how cells separate, grow, and resist different stresses. In 2009, a novel RNA technology, termed ribosome profiling, was invented by Dr. Jonathan Weissman Lab from UCSF. Ribosome profiling (Ribo-Seq) is a powerful tool which can provide the most direct readout of the intracellular translation state of a protein including information on the location of translation start/stop sites, ribosome distribution pattern, and even the moving rate of the translating ribosome, at the whole-genome scale and single-nucleotide resolution.

To date, many researchers including our lab have successfully applied ribosome profiling method for diverse purposes. We thus review in this chapter the underlying mechanism and recent advances as regards this fantastic tool. Firstly, we introduce the working mechanism, advantages, and study history of ribosome profiling. Secondly, we discuss the data analysis pipeline, also compare different statistical algorithms and data visualization software. Finally, we review the extensive applications of Ribo-seq, for example, identification of uORF, computation of global translation efficiency (TE), the study of the posttranscriptional regulatory role of RNA binding protein and others. We hope this chapter would be useful for interested systems biology researchers as well as RNA biologists.

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Acknowledgements

We apologize for not being able to cite many works owing to lack of space.

Author information

Authors and Affiliations

  1. Division of Infectious Diseases, Weill Medical College of Cornell University, New York, NY, USA

    Zhe Wang

  2. Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA

    Zhenglong Gu

Authors
  1. Zhe Wang
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  2. Zhenglong Gu
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Corresponding author

Correspondence to Zhe Wang .

Editor information

Editors and Affiliations

  1. Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin-Buch, Berlin, Germany

    Nikolaus Rajewsky

  2. Nanobiomedical Center, Adam Mickiewicz University, Poznań, Poland

    Stefan Jurga

  3. Polish Academy of Sciences, Institute of Bioorganic Chemistry, Poznań, Poland

    Jan Barciszewski

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Wang, Z., Gu, Z. (2018). Novel Insights of the Gene Translational Dynamic and Complex Revealed by Ribosome Profiling. In: Rajewsky, N., Jurga, S., Barciszewski, J. (eds) Systems Biology. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-319-92967-5_12

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