Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs.

ABSTRACT:

Background

Sequence specific RNA binding proteins are important regulators of gene expression. Several related crosslinking-based, high-throughput sequencing methods, including PAR-CLIP, have recently been developed to determine direct binding sites of global protein-RNA interactions. However, no studies have quantitatively addressed the contribution of background binding to datasets produced by these methods.

Results

We measured non-specific RNA background in PAR-CLIP data, demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal among laboratories. We show that quantitative determination of background is essential for identifying targets of most RNA-binding proteins and can substantially improve motif analysis. We also d

SUBMITTER: Friedersdorf MB 

PROVIDER: S-EPMC4053780 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature