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

E Ransey, Anders Björkbom, VS Lelyveld, P Biecek, L Pantano, JW Szostak, P Sliz

Research output: Contribution to journalArticleScientificpeer-review

5 Citations (Scopus)

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.
Original languageUndefined/Unknown
Pages (from-to)1756–1765
Number of pages10
JournalRNA Biology
Volume14
Issue number12
DOIs
Publication statusPublished - 2017
MoE publication typeA1 Journal article-refereed

Keywords

  • CLIP
  • CIMS
  • LIN28

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