LaceSeq
26 March 2024
Phospho-RNA sequencing with circAID-p-seq
![](https://www.immaginabiotech.com/media/7b/ff/0b/1709824134/delpiano_NAR.webp)
Del Piano A, Kecman T, Schmid M, Barbieri R, Brocchieri L, Tornaletti S, Firrito C, Minati L, Bernabo P, Signoria I, Lauria F, Gillingwater TH, Viero G, Clamer M. Phospho-RNA sequencing with circAID-p-seq. Nucleic Acids Res. 2022 Feb 28;50(4):e23. doi: 10.1093/nar/gkab1158. PMID: 34850942; PMCID: PMC8887461.
Most RNA footprinting approaches that require ribonuclease cleavage generate RNA fragments bearing a phosphate or cyclic phosphate group at their 3' end. Unfortunately, current library preparation protocols rely only on a 3' hydroxyl group for adaptor ligation or poly-A tailing. Here, we developed circAID-p-seq, a PCR-free library preparation for selective 3' phospho-RNA sequencing. As a proof of concept, we applied circAID-p-seq to ribosome profiling, which is based on sequencing of RNA fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast and highly efficient sequencing of phospho-RNA fragments from eukaryotic cells and tissues. We used circAID-p-seq to portray ribosome occupancy in transcripts, providing a versatile and PCR-free strategy to possibly unravel any endogenous 3'-phospho RNA molecules.
Keywords: 3' phospho-RNA, Ribosome profiling, Phospho-RNA fragments, library preparation