Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads

MicroRNA (miRNA) trans-regulates the stability of many mRNAs and controls their expression levels. Reconstruction of the miRNA-mRNA interactome is key to the understanding of the miRNA regulatory network and related biological processes. However, existing miRNA target prediction methods are limited to canonical miRNA-mRNA interactions and have high false prediction rates. Other experimental methods are low throughput and cannot be used to probe genome-wide interactions. To address this challenge, the Cross-linking Ligation and Sequencing of Hybrids (CLASH) technology was developed for high-throughput probing of transcriptome-wide microRNA-mRNA interactions in vivo. The mapping of duplex reads, chimeras of two ultra-short RNA strands, poses computational challenges to current mapping and alignment methods. To address this issue, we developed CLAN (CrossLinked reads ANalysis toolkit). CLAN generated a comparable mapping of singular reads to other tools, and significantly outperformed in mapping simulated and real CLASH duplex reads, offering a potential application to other next-generation sequencing-based duplex-read-generating technologies.