Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq.

ABSTRACT: RNA-binding proteins (RBPs) and noncoding RNAs orchestrate post-transcriptional processes through the recognition of specific sites on targeted transcripts. Thus, understanding the connection between binding to specific sites and active regulation of the whole transcript is essential. Many immunoprecipitation techniques have been developed that identify either whole transcripts or binding sites of RBPs on each transcript using cell lysates. However, none of these methods simultaneously measures the strength of each binding site and quantifies binding to whole transcripts. In this study, we compare current procedures and present digestion optimized (DO)-RIP-seq, a simple method that locates and quantifies RBP binding sites using a continuous metric. We have used the RBP HuR/ELAVL1 to demons

SUBMITTER: Nicholson CO 

PROVIDER: S-EPMC5159647 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature