Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

ABSTRACT: Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples sequencing on an Illumina GAIIx genome analyzer with the quantitative assessment of protein-RNA interactions. This assay is able to analyze interactions between one or possibly several proteins with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of the EGFP and negative elongation factor subunit E (NELF-E) proteins with their corresponding canonical and mutant RNA aptamers. Here we provide a detailed protocol for Hi

SUBMITTER: Ozer A 

PROVIDER: S-EPMC4714542 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature