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Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads
dc.contributor.author | Zhong, Cuncong | |
dc.contributor.author | Zhang, Shaojie | |
dc.date.accessioned | 2021-01-13T17:17:56Z | |
dc.date.available | 2021-01-13T17:17:56Z | |
dc.date.issued | 2019-05-28 | |
dc.identifier.citation | Zhong, C., & Zhang, S. (2019, August 30). Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads. iScience, 18, 11-19. | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/31127 | |
dc.description | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | en_US |
dc.description.abstract | 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. | en_US |
dc.publisher | Cell Press | en_US |
dc.rights | © 2019 The Author(s). | en_US |
dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | en_US |
dc.title | Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Zhong, Cuncong | |
kusw.kudepartment | Electrical Engineering & Computer Science | en_US |
dc.identifier.doi | 10.1016/j.isci.2019.05.038 | en_US |
kusw.oaversion | Scholarly/refereed, publisher version | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.rights.accessrights | openAccess | en_US |