Journal article
Sequencing of captive target transcripts identifies the network of regulated genes and functions of rimate-specific miR-522
SM Tan, R Kirchner, J Jin, O Hofmann, L McReynolds, W Hide, J Lieberman
Cell Reports | CELL PRESS | Published : 2014
Open access
Abstract
Identifying microRNA (miRNA)-regulated genes is key to understanding miRNA function. However, many miRNA recognition elements (MREs) do not follow canonical "seed" base-pairing rules, making identification of bona fide targets challenging. Here, we apply an unbiased sequencing-based systems approach to characterize miR-522, a member of the oncogenic primate-specific chromosome 19 miRNA cluster, highly expressed in poorly differentiated cancers. To identify miRNA targets, we sequenced full-length transcripts captured by a biotinylated miRNA mimic. Within these targets, mostly noncanonical MREs were identified by sequencing RNase-resistant fragments. miR-522 overexpression reduced mRNA, protei..
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Awarded by National Institute of Child Health and Human Development
Funding Acknowledgements
We thank J.L. laboratory members for critical discussions. S.M.T. is supported by the Department of Defense Breast Cancer Research Program. Microarray experiments were performed by the Molecular Genetics Core Facility at Boston Children's Hospital supported by NIH-P50-NS40828 and NIH-P30-HD18655. The bioinformatics analyses, supported by the HSCI Center of Stem Cell Bioinformatics, were run on the Odyssey cluster supported by the Harvard University FAS Research Computing Group. J.J. and L.M. are employees of New England Biolabs, a company that sells deep sequencing kits for RNA and DNA research.