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Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions
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  • Published: 30 March 2017

Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions

  • Krishna Choudhary1,
  • Fei Deng1 &
  • Sharon Aviran1 

Quantitative Biology volume 5, pages 3–24 (2017)Cite this article

  • 1012 Accesses

  • 17 Citations

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Abstract

Background

Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data.

Results

We review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy.

Conclusions

To keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.

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Acknowledgments

This work was supported by the National Institutes of Health (NIH) grant (No. HG006860). We thank Chun Kit Kwok and Aviran lab members — Mirko Ledda, Sana Vaziri, Hua Li and Rob Gysel — for insightful comments during the preparation of this manuscript.

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  1. Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, 95616, USA

    Krishna Choudhary, Fei Deng & Sharon Aviran

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  1. Krishna Choudhary
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Correspondence to Sharon Aviran.

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This article is dedicated to the Special Collection of Synthetic Biology, Aiming for Quantitative Control of Cellular Systems (Eds. Cheemeng Tan and Haiyan Liu).

These authors contributed equally to this work.

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Choudhary, K., Deng, F. & Aviran, S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. Quant Biol 5, 3–24 (2017). https://doi.org/10.1007/s40484-017-0093-6

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  • Received: 02 October 2016

  • Revised: 08 December 2016

  • Accepted: 15 December 2016

  • Published: 30 March 2017

  • Issue Date: March 2017

  • DOI: https://doi.org/10.1007/s40484-017-0093-6

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Keywords

  • RNA structure profiling
  • high-throughput sequencing
  • RNA secondary structure prediction
  • chemical structure probing
  • SHAPE-Seq
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