Genome-Wide Decoding of mRNP and miRNA Maps

The limited number of primary transcripts in the genome has promoted interest in the possibility that much of the complexity in the regulation of gene expression may be determined by RNA regulation controlled by RNA-binding proteins (RNABPs) and/or microRNAs (miRNAs). However, applying biochemical methods to understand such interactions in living tissues is major challenge. Here we developed a genome-wide means of mapping messenger ribonucleoprotein (mRNP) sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova provides genome-wide maps of Nova-RNA interactions in vivo and leads to a new finding that Nova may regulate the processesing of some miRNAs. Furthermore, HITS-CLIP analysis is extended to the problem of identifying miRNA targets, for which prediction is a major challenge since miRNA activity requires base pairing through only 6-8 “seed†nucleotides. By generating crosslinking of native Argonaute (Ago) protein-RNA complexes in mouse brain, Ago HITS-CLIP produced two simultaneous datasets—Ago-miRNA and Ago-mRNA binding sites—that were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. We also found that the relatively large number of Ago proteins bind in coding sequence, as well as introns, suggesting unexplored functions for miRNAs. Not all Ago mRNA clusters correspond to known seed sequence, leading to the discovery of putative new rules for miRNA-mRNA interactions. HITS-CLIP provides a general plaform to identify functional mRNP and miRNA binding sites in vivo and a solution to determining precise sequences for targeting clinically relevant sites of RNA regulation. In addition, overlaying mRNP maps with miRNA maps will be informative for the understanding of RNA regulations and complexity