Phospho-RNA sequencing with circAID-p-seq

by Del Piano, Alessia; Kecman, Tea; Schmid, Michael; Barbieri, Ruggero; Brocchieri, Luciano; Tornaletti, Silvia; Firrito, Claudia; Minati, Luca; Bernabo, Paola; Signoria, Ilaria; Lauria, Fabio; Gillingwater, Thomas H; Viero, Gabriella and Clamer, Massimiliano
Abstract:
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.
Reference:
Phospho-RNA sequencing with circAID-p-seq (Del Piano, Alessia; Kecman, Tea; Schmid, Michael; Barbieri, Ruggero; Brocchieri, Luciano; Tornaletti, Silvia; Firrito, Claudia; Minati, Luca; Bernabo, Paola; Signoria, Ilaria; Lauria, Fabio; Gillingwater, Thomas H; Viero, Gabriella and Clamer, Massimiliano), In Nucleic Acids Research, 2021.
Bibtex Entry:
@article{10.1093/nar/gkab1158,
    author = {Del Piano, Alessia and Kecman, Tea and Schmid, Michael and Barbieri, Ruggero and Brocchieri, Luciano and Tornaletti, Silvia and Firrito, Claudia and Minati, Luca and Bernabo, Paola and Signoria, Ilaria and Lauria, Fabio and Gillingwater, Thomas H and Viero, Gabriella and Clamer, Massimiliano},
    title = "{Phospho-RNA sequencing with circAID-p-seq}",
    journal = {Nucleic Acids Research},
    year = {2021},
    month = {12},
    abstract = "{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.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkab1158},
    url = {https://doi.org/10.1093/nar/gkab1158},
    note = {gkab1158},
    eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkab1158/41426377/gkab1158.pdf},
}