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

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.

Graphical abstract

Keywords

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

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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.

COMPLIANCE WITH ETHICS GUIDELINES

Krishna Choudhary, Fei Deng and Sharon Aviran declare that they have no conflict of interest.ƒ€This article does not contain any studies with human or animal subjects performed by any of the authors.

Funding

RIGHTS & PERMISSIONS

2017 Higher Education Press and Springer-Verlag Berlin Heidelberg