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

Krishna Choudhary, Fei Deng, Sharon Aviran

Research output: Contribution to journalReview article

17 Citations (Scopus)

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. [Figure not available: see fulltext.].

Original languageEnglish (US)
Pages (from-to)3-24
Number of pages22
JournalQuantitative Biology
Volume5
Issue number1
DOIs
StatePublished - Mar 1 2017

Fingerprint

Profiling
RNA
Gene Expression Profiling
Nucleotides
Transcriptome
Cells
Throughput
Technology
Structure Prediction
Experiments
Comparative Analysis
Chemistry
Sequencing
High Throughput
Biology
Figure
Complement
Methodology
Prediction
Cell

Keywords

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

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computer Science Applications
  • Modeling and Simulation
  • Applied Mathematics

Cite this

Comparative and integrative analysis of RNA structural profiling data : current practices and emerging questions. / Choudhary, Krishna; Deng, Fei; Aviran, Sharon.

In: Quantitative Biology, Vol. 5, No. 1, 01.03.2017, p. 3-24.

Research output: Contribution to journalReview article

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N2 - 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. [Figure not available: see fulltext.].

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