CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Chang, Hong ^a   Yi, Bin ^a   Ma, Ruixia ^a   Zhang, Xiaoguo ^a   Zhao, Hongyou ^a   Xi, Yaguang ^a  

^a UNIVERSITY OF SOUTH ALABAMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUIDE RNA; MICRORNA;

ANIMAL; CELL LINE; CHEMISTRY; CRISPR CAS SYSTEM; GENE EDITING; GENE SILENCING; GENE TARGETING; GENETICS; GENOMICS; HUMAN; INDEL MUTATION; MOUSE; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROCEDURES; RNA EDITING; RNA STABILITY;

ANIMALS; BASE SEQUENCE; CELL LINE; CRISPR-CAS SYSTEMS; GENE EDITING; GENE KNOCKDOWN TECHNIQUES; GENE TARGETING; GENOMICS; HUMANS; INDEL MUTATION; MICE; MICRORNAS; PHENOTYPE; RNA EDITING; RNA STABILITY; RNA, GUIDE;

EID: 84988642880     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep22312     Document Type: Article

References (35)

1. Bassett, A. R. et al. Understanding functional miRNA-target interactions in vivo by site-specific genome engineering. Nat Commun 5, 4640 (2014).
2. Feng, X., Wang, Z., Fillmore, R. & Xi, Y. MiR-200, a new star miRNA in human cancer. Cancer Lett 344, 166-173 (2014).
3. Ernst, A. et al. De-repression of CTGF via the miR-17-92 cluster upon differentiation of human glioblastoma spheroid cultures. Oncogene 29, 3411-3422 (2010).
4. Ebert, M. S., Neilson, J. R. & Sharp, P. A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4, 721-726 (2007).
5. Bhaya, D., Davison, M. & Barrangou, R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45, 273-297 (2011).
6. Brouns, S. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964 (2008).
7. Mali, P., Esvelt, K. M. & Church, G. M. Cas9 as a versatile tool for engineering biology. Nat Methods 10, 957-963 (2013).
8. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
9. Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910-918 (2013).
10. Gao, Y. et al. Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development. Proc Natl Acad Sci USA 112, 2275-2280 (2015).
11. Friedland, A. E. et al. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10, 741-743 (2013).
12. Ren, X. et al. Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep 9, 1151-1162 (2014).
13. Matano, M. et al. Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids. Nat Med 21, 256-262 (2015).
14. Zeng, Y., Yi, R. & Cullen, B. R. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J 24, 138-148 (2005).
15. Burk, U. et al. A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells. EMBO Rep 9, 582-589 (2008).
16. Reyon, D. et al. FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30, 460-465 (2012).
17. Burke, J. M., Kelenis, D. P., Kincaid, R. P. & Sullivan, C. S. A central role for the primary microRNA stem in guiding the position and efficiency of Drosha processing of a viral pri-miRNA. RNA 20, 1068-1077 (2014).
18. Medina, P. P. & Slack, F. J. Inhibiting microRNA function in vivo. Nat Methods 6, 37-38 (2009).
19. Kluiver, J. et al. Rapid generation of microRNA sponges for microRNA inhibition. PLoS One 7, e29275 (2012).
20. Kauppinen, S., Vester, B. & Wengel, J. Locked nucleic acid (LNA): High affinity targeting of RNA for diagnostics and therapeutics. Drug Discov Today Technol 2, 287-290 (2005).
21. Ebert, M. S. & Sharp, P. A. MicroRNA sponges: progress and possibilities. RNA 16, 2043-2050 (2010).
22. Gaj, T., Gersbach, C. A. & Barbas, C. F., 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31, 397-405 (2013).
23. Niu, Y. et al. Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos. Cell 156, 836-843 (2014).
24. Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87 (2014).
25. Takada, S. et al. Targeted gene deletion of miRNAs in mice by TALEN system. PLoS One 8, e76004 (2013).
26. Zhang, Z. et al. Dissecting the Roles of miR-302/367 Cluster in Cellular Reprogramming Using TALE-based Repressor and TALEN. Stem Cell Reports 1, 218-225 (2013).
27. Zhao, Y. et al. Sequence-specific inhibition of microRNA via CRISPR/CRISPRi system. Sci Rep 4, 3943 (2014).
28. Jiang, Q. et al. Small indels induced by CRISPR/Cas9 in the 5′ region of microRNA lead to its depletion and Drosha processing retardance. RNA Biol 11, 1243-1249 (2014).
29. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415-419 (2003).
30. Kim, Y. K. et al. TALEN-based knockout library for human microRNAs. Nat Struct Mol Biol 20, 1458-1464 (2013).
31. Sapranauskas, R. et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39, 9275-9282 (2011).
32. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
33. Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31, 822-826 (2013).
34. Veres, A. et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 15, 27-30 (2014).
35. Guschin, D. Y. et al. A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol 649, 247-256 (2010).