PARE-Seq
PARE-Seq
Various RNA degradation processes impart characteristic sequence ends. By analyzing the cleavage sites, the degradation processes can be inferred. In PARE-Seq, the degraded uncapped mRNA is ligated to 5' adapters containing an MmeI restriction site and reverse-transcribed. The cDNA fragments are digested with Mmel, purified, ligated to 3' adapters, and PCR-amplified. Deep sequencing of the cDNA provides information about uncapped transcripts that undergo degradation.
Pros:
- Maps degrading RNA
- miRNA cleavage sites are identified
- No prior knowledge of the target RNA sequence is required
Cons:
- Non-linear PCR amplification can lead to biases affecting reproducibility
- Amplification errors caused by polymerases will be represented and sequenced incorrectly