PARE-Seq

PARE-Seq

Parallel analysis of RNA ends sequencing (PARE-Seq) maps miRNA cleavage sites. Various RNA degradation processes impart characteristic sequence ends. By analyzing the cleavage sites, the degradation processes can be inferred. In this method, degraded capped mRNA is adapter-ligated and reverse-transcribed. Fragments are then Mmel-digested, purified, 3’-adapter-ligated, 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 ot biases affecting reproducibility
• Amplification errors caused by polymerases will be represented and sequenced incorrectly

• PARE-Seq: German M. A., Pillay M., Jeong D. H., Hetawal A., Luo S., et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26: 941-946

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3. Dotto M. C., Petsch K. A., Aukerman M. J., Beatty M., Hammell M., et al. (2014) Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development. PLoS Genet 10: e1004826
4. Gai Y. P., Li Y. Q., Guo F. Y., Yuan C. Z., Mo Y. Y., et al. (2014) Analysis of phytoplasma-responsive sRNAs provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease. Sci Rep 4: 5378
5. Kakrana A., Hammond R., Patel P., Nakano M. and Meyers B. C. (2014) sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. Nucleic Acids Res 42: e139
6. Zhai J., Arikit S., Simon S. A., Kingham B. F. and Meyers B. C. (2014) Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods 67: 84-90