CIP-TAP
CIP-TAP
Alkaline phosphatase, calf intestine-tobacco acid pyrophosphatase sequencing (CIP-TAP) maps capped small RNAs . In this method, RNA is treated with CIP followed by 3’-end linker ligation, then treated with TAP followed by 5’-end linker ligation. The fragments are then reverse-transcribed to cDNA, PCR-amplified, and sequenced. Deep sequencing provides single-nucleotide resolution reads of the capped small RNAs.
Pros:
- Identifies capped small RNAs missed by CAP-Seq
- Hight throughput
Cons:
- Non-linear PCR amplification can lead to biases affecting reproducibility
- Amplification errors caused by polymerases
- Tobacco Acid Pyrophosphatase (TAP)
- Calf Intestinal Phosphatase (CIP)
- APex Heat-Labile Alkaline Phosphatase
- Xie M., Li M., Vilborg A., Lee N., Shu M. D., et al. (2013) Mammalian 5'-capped microRNA precursors that generate a single microRNA. Cell 155: 1568-1580.
- Gu W., Lee H. C., Chaves D., Youngman E. M., Pazour G. J., et al. (2012) CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell 151: 1488-1500.
- Yang L., Lin C., Jin C., Yang J. C., Tanasa B., et al. (2013) lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. Nature 500: 598-602