Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing

Part of the Methods in Molecular Biology book series (MIMB, volume 1361)


RNA structure probing is an important technique that studies the secondary and tertiary conformations of an RNA. While it was traditionally performed on one RNA at a time, recent advances in deep sequencing has enabled the secondary structure mapping of thousands of RNAs simultaneously. Here, we describe the method Parallel Analysis for RNA Structures (PARS), which couples double and single strand specific nuclease probing to high throughput sequencing. Upon cloning of the cleavage sites into a cDNA library, deep sequencing and mapping of reads to the transcriptome, the position of paired and unpaired bases along cellular RNAs can be identified. PARS can be performed under diverse solution conditions and on different organismal RNAs to provide genome-wide RNA structural information. This information can also be further used to constrain computational predictions to provide better RNA structure models under different conditions.

Key words

RNA Structure Biochemistry Genomics High-throughput sequencing 



This work is supported by NIH R01-HG004361 (H.Y.C.) and Agency for Science, Technology and Research of Singapore (Y.W.).


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Stem Cell and Developmental BiologyGenome Institute of SingaporeSingaporeSingapore
  2. 2.Howard Hughes Medical Institute and Program in Epithelial BiologyStanford University School of MedicineStanfordUSA
  3. 3.The Jackson Laboratory for Genomic MedicineFarmingtonUSA
  4. 4.Department of Biomedical EngineeringUniversity of ConnecticutStorrsUSA

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