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High-Throughput Nuclease Probing of RNA Structures Using FragSeq

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RNA Structure Determination

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1490))

Abstract

High-throughput sequencing of cDNA (RNA-Seq) can be used to generate nuclease accessibility data for many distinct transcripts in the same mixture simultaneously. Such assays accelerate RNA structure analysis and provide researchers with new technologies to tackle biological questions on a transcriptome-wide scale. FragSeq is an experimental assay for transcriptome-wide RNA structure probing using RNA-Seq, coupled with data analysis tools that allow quantitative determination of nuclease accessibility at single-base resolution. We provide a practical guide to designing and carrying out FragSeq experiments and data analysis.

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Acknowledgements

We thank David H. Mathews for the invitation to write this chapter. We also thank John St. John, Yann Ponty, and Lukasz J. Kielpinski for helpful discussions.

Author information

Authors and Affiliations

  1. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Andrew V. Uzilov

  2. Research and Development, Pacific Biosciences, Menlo Park, CA, USA

    Jason G. Underwood

Authors
  1. Andrew V. Uzilov
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  2. Jason G. Underwood
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Corresponding author

Correspondence to Andrew V. Uzilov .

Editor information

Editors and Affiliations

  1. Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, New York, USA

    Douglas H. Turner

  2. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA

    David H. Mathews

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Uzilov, A.V., Underwood, J.G. (2016). High-Throughput Nuclease Probing of RNA Structures Using FragSeq. In: Turner, D., Mathews, D. (eds) RNA Structure Determination. Methods in Molecular Biology, vol 1490. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6433-8_8

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  • DOI: https://doi.org/10.1007/978-1-4939-6433-8_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6431-4

  • Online ISBN: 978-1-4939-6433-8

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