Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution.
Elizabeth RanseyAnders BjörkbomVictor S LelyveldPrzemysław BiecekLorena PantanoJack W SzostakPiotr SlizPublished in: RNA biology (2017)
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.
Keyphrases
- ms ms
- tandem mass spectrometry
- ultra high performance liquid chromatography
- high performance liquid chromatography
- liquid chromatography
- simultaneous determination
- single cell
- gas chromatography
- single molecule
- mass spectrometry
- high resolution
- high glucose
- drug induced
- high resolution mass spectrometry
- endothelial cells