Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution
| Autor: | Victor S. Lelyveld, Piotr Sliz, Elizabeth Ransey, Przemyslaw Biecek, Lorena Pantano, Anders Björkbom, Jack W. Szostak |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Models Molecular Immunoprecipitation Guanine Protein Conformation RNA-binding protein Computational biology macromolecular substances Biology Tandem mass spectrometry Deep sequencing Mass Spectrometry 03 medical and health sciences chemistry.chemical_compound RNA Precursors Humans Nucleotide Binding site Molecular Biology chemistry.chemical_classification Genetics Binding Sites CIMS technology industry and agriculture RNA CLIP RNA-Binding Proteins Cell Biology Recombinant Proteins LIN28 MicroRNAs 030104 developmental biology chemistry Mutation Nucleic Acid Conformation Research Paper Protein Binding |
| Zdroj: | RNA Biology |
| ISSN: | 1555-8584 1547-6286 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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