Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution
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CitationRansey, Elizabeth, Anders Björkbom, Victor S. Lelyveld, Przemyslaw Biecek, Lorena Pantano, Jack W. Szostak, and Piotr Sliz. 2017. “Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution.” RNA Biology 14 (12): 1756-1765. doi:10.1080/15476286.2017.1356566. http://dx.doi.org/10.1080/15476286.2017.1356566.
AbstractABSTRACT 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.
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