A biochemical approach to identifying microRNA targets
Abstract
Identifying the downstream targets of microRNAs (miRNAs) is essential to understanding cellular regulatory networks. We devised a direct biochemical method for miRNA target discovery that combined RNA-induced silencing complex (RISC) purification with microarray analysis of bound mRNAs. Because targets of miR-124a have been analyzed, we chose it as our model. We honed our approach both by examining the determinants of stable binding between RISC and synthetic target RNAs in vitro and by determining the dependency of both repression and RISC coimmunoprecipitation on miR-124a seed sites in two of its well characterized targets in vivo . Examining the complete spectrum of miR-124 targets in 293 cells yielded both a set that were down-regulated at the mRNA level, as previously observed, and a set whose mRNA levels were unaffected by miR-124a. Reporter assays validated both classes, extending the spectrum of mRNA targets that can be experimentally linked to the miRNA pathway.
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No change of Ago2 function has been reported due to fusion with an epitope tag.
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From Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain (2012) · cites this paper as Karginov et al., 2007
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Wightman, B., Ha, I., & Ruvkun, G. (1993) · Cell · doi:10.1016/0092-8674(93)90530-4 · Cited by 4,292 · see citing works
Stark, A., Brennecke, J., Bushati, N., Russell, R. B., & Cohen, S. M. (2005) · Cell · doi:10.1016/j.cell.2005.11.023 · Cited by 1,080 · see citing works
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- [24]Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY). 19296 www.pnas.orgcgidoi10.1073pnas.0709971104 Karginov et al.
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Self-citationCell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain
He, M., Liu, Y., Wang, X., Zhang, M. Q., Hannon, G. J., & Huang, Z. J. (2012) · Neuron · doi:10.1016/j.neuron.2011.11.010 · Cited by 277 · see citing works
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Karali, M., Manfredi, A., Puppo, A., Marrocco, E., Gargiulo, A., Allocca, M., Corte, M. D., Rossi, S., Giunti, M., Bacci, M. L., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022166 · Cited by 60 · see citing works
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- Authors
- Karginov, F. V., Conaco, C., Xuan, Z., Schmidt, B. H., Parker, J. S., Mandel, G., & Hannon, G. J.
- Affiliations
- *Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724;
- Department of Neurobiology and Behavior, Howard Hughes Medical Institute, State University of New York, Stony Brook, NY 11794; and
- Expression Analysis, Inc., 4324 South Alston Avenue, Durham, NC 27713
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2007-12-04
- Volume
- 104
- Issue
- 49
- Pages
- 19291-19296
- ISSN
- 0027-8424
- 1091-6490
- Cited by
- 302
- References
- 2
- Language
- en
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