TRAP-SEQ of eukaryotic translatomes applied to the detection of polysome-associated long non-coding RNAs

FLAVIO ANTONIO BLANCO; MARÍA EUGENIA ZANETTI; SOLEDAD TRAUBENIK; MAURICIO ALBERTO REYNOSO

RNA Tagging: Methods and Protocols

Springer

Año: 2020; p. 453 - 474

Translating Ribosome Affinity Purification (TRAP) technology allows the isolation of polysomal complexes and the RNAs associated with at least one 80S ribosome. TRAP consists of the stabilization and affinity purification of polysomes containing a tagged version of a ribosomal protein. Quantitative assessment of the TRAP RNA is achieved by direct sequencing (TRAP-SEQ), which provides accurate quantitation of ribosome-associated RNAs, including long non-coding RNAs (lncRNAs). Here we present an updated procedure for TRAP-SEQ, as well as a primary analysis guide for identification of ribosome-associated lncRNAs. This methodology enables the study of dynamic association of lncRNAs by assessing rapid changes in their transcript levels in polysomes at organ or cell-type level, during development, or in response to endogenous or exogenous stimuli.