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

A1 Journal article (refereed)


Internal Authors/Editors


Publication Details

List of Authors: Ransey E, Björkbom A, Lelyveld VS, Biecek P, Pantano L, Szostak JW, Sliz P
Publisher: TAYLOR & FRANCIS INC
Publication year: 2017
Journal: RNA Biology
Journal acronym: RNA BIOL
Volume number: 14
Issue number: 12
Start page: 1756
End page: 1765
Number of pages: 10
ISSN: 1547-6286


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.


Keywords

CIMS, CLIP, LIN28

Last updated on 2019-21-09 at 03:08