PARS/dsRNA-Seq

PARS/dsRNA-Seq

Parallel analysis of RNA structure (PARS-Seq)  mapping gives information about the secondary and tertiary structure of RNA. In this method RNA is digested with RNases that are specific for double-stranded and single-stranded RNA, respectively. The resulting fragments are reverse-transcribed to cDNA. Deep sequencing of the cDNA provides high-resolution sequences of the RNA. The RNA structure can be deduced by comparing the digestion patterns of the various RNases.

Pros:

• Provides RNA structural information
• Distinguishes between paired and unpaired bases
• Alternative to mass spectrometry, NMR, and crystallography

Cons:

• Enzyme digestion can be nonspecific
• Digestion conditions must be carefully controlled
• RNA can be over-digested

• PARS-Seq/dsRNA-Seq: Wan Y., Qu K., Ouyang Z. and Chang H. Y. (2013) Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat Protoc 8: 849-869

1. Sugimoto Y., Vigilante A., Darbo E., Zirra A., Militti C., et al. (2015) hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature 519: 491-494.
2. Wan Y, Qu K, Ouyang Z, Chang HY; (2013) Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat Protoc 8: 849-69