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Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution.

ABSTRACT: It remains a formidable challenge to characterize the diverse complexes of RNA binding proteins and their targets. While crosslink and immunoprecipitation (CLIP) methods are powerful techniques that identify RNA targets on a global scale, the resolution and consistency of these methods is a matter of debate. Here we present a comparative analysis of LIN28-pre-let-7 UV-induced crosslinking using a tandem mass spectrometry (MS/MS) and deep sequencing interrogation of in vitro crosslinked complexes. Interestingly, analyses by the two methods diverge in their identification of crosslinked nucleotide identity - whereas bioinformatics and sequencing analyses suggest guanine in mammalian cells, MS/MS identifies uridine. This work suggests the need for comprehensive analysis and validation of crosslinking methodologies.

SUBMITTER: Ransey E

PROVIDER: S-EPMC5731800 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution.

Ransey Elizabeth E Björkbom Anders A Lelyveld Victor S VS Biecek Przemyslaw P Pantano Lorena L Szostak Jack W JW Sliz Piotr P

RNA biology 20171009 12

It remains a formidable challenge to characterize the diverse complexes of RNA binding proteins and their targets. While crosslink and immunoprecipitation (CLIP) methods are powerful techniques that identify RNA targets on a global scale, the resolution and consistency of these methods is a matter of debate. Here we present a comparative analysis of LIN28-pre-let-7 UV-induced crosslinking using a tandem mass spectrometry (MS/MS) and deep sequencing interrogation of in vitro crosslinked complexes ...[more]

PMID: 28945502

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