Dataset Information

Phospho-RNA sequencing with circAID-p-seq.

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.

SUBMITTER: Del Piano A

PROVIDER: S-EPMC8887461 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Publications

Phospho-RNA sequencing with circAID-p-seq.

Del Piano Alessia A Kecman Tea T Schmid Michael M Barbieri Ruggero R Brocchieri Luciano L Tornaletti Silvia S Firrito Claudia C Minati Luca L Bernabo Paola P Signoria Ilaria I Lauria Fabio F Gillingwater Thomas H TH Viero Gabriella G Clamer Massimiliano M

Nucleic acids research 20220201 4

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 fragmen ...[more]

PMID: 34850942

Dataset Information

Phospho-RNA sequencing with circAID-p-seq.

Publications

Phospho-RNA sequencing with circAID-p-seq.

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