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Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions |
Krishna Choudhary,Fei Deng,Sharon Aviran( ) |
Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA 95616, USA |
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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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Author Summary RNAs are known to play essential roles in diverse cellular functions, extending well-beyond transfer of information from genes to proteins. RNA function is closely linked to its ability to fold into and convert between specific complex structures. Determining RNA structure has thus become a crucial step in understanding its function. Structure profiling experiments provide single nucleotide information on RNA structure. Recent advances in chemistry combined with application of new high-throughput sequencing techniques have enabled RNA structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. In this paper, we review current practices in analysis of structure profiling data, with emphasis on comparative and integrative analysis, as well as highlight emerging questions. |
Keywords
RNA structure profiling
high-throughput sequencing
RNA secondary structure prediction
chemical structure probing
SHAPE-Seq
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Fund: |
Corresponding Author(s):
Sharon Aviran
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Online First Date: 24 January 2017
Issue Date: 22 March 2017
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