Endoribonuclease-prepared siRNA
esiRNA or Endoribonuclease-prepared siRNAs are a mixture of siRNA oligos resulting from cleavage of long double-stranded RNA (dsRNA) with an endoribonuclease such as Escherichia coli RNase III or Dicer.[1][2]
An alternative concept to the usage of chemically synthesized siRNA for RNA Interference (RNAi) is the enzymatic digestion of long double stranded RNAs in vitro. In this case a cDNA template is amplified by PCR and tagged with two bacteriophage-promoter sequences. RNA polymerase is then used to generate long double stranded RNA that is homologous to the target-gene cDNA. This RNA is subsequently digested with RNase III from Escherichia coli to generate short overlapping fragments of siRNAs with a length between 18-25 base pairs. This complex mixture of short double stranded RNAs is similar to the mixture generated by Dicer cleavage in vivo and is therefore called endoribonuclease-prepared siRNA or short esiRNA. esiRNA are a heterogeneous mixture of siRNAs that all target the same mRNA sequence. These multiple silencing triggers lead to highly specific and effective gene silencing.[2]
References
- Blow, Nathan (2008). "RNAi technologies: a screen whose time has arrived". Nature Methods. 5 (4): 361–368. doi:10.1038/nmeth0408-361.
- Kittler, R; Pelletier, L (2004). "An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division". Nature. 432 (7020): 1036–1040. Bibcode:2004Natur.432.1036K. doi:10.1038/nature03159. PMID 15616564. S2CID 4372785.
- Lawo et al. HAUS, the 8-Subunit Human Augmin Complex, Regulates Centrosome and Spindle Integrity. Curr Biol. 2009; 19:816-26 (2009).
- Ding et al. A Genome-Scale RNAi Screen for Oct4 Modulators Defines a Role of the Paf1 Complex for Embryonic Stem Cell Identity. Cell Stem Cell. Apr (2009)
- Theis et al. Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. EMBO J. Apr 23 (2009).
- Stewart; et al. (2009). "The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage". Cell. 136 (3): 420–34. doi:10.1016/j.cell.2008.12.042. PMID 19203578. S2CID 12683637.
- Kittler, R.; et al. (2007). "Genome-scale RNAi profiling of cell division in human tissue culture cells". Nat. Cell Biol. 9 (12): 1401–12. doi:10.1038/ncb1659. PMID 17994010. S2CID 22304252.
- Kittler, R.; et al. (2007). "Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies". Nat. Methods. 4 (4): 337–44. doi:10.1038/nmeth1025. PMID 17351622. S2CID 8554458.
- Konstantinova; et al. (2007). "EphA-Ephrin-A-mediated beta cell communication regulates insulin secretion from pancreatic islets". Cell. 129 (2): 359–70. doi:10.1016/j.cell.2007.02.044. PMID 17448994. S2CID 8701076.
- Nikolova; et al. (2006). "The vascular basement membrane: a niche for insulin gene expression and Beta cell proliferation". Dev Cell. 10 (3): 397–405. doi:10.1016/j.devcel.2006.01.015. PMID 16516842.
- Kittler; et al. (2005). "RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells". Proc Natl Acad Sci U S A. 102 (7): 2396–401. Bibcode:2005PNAS..102.2396K. doi:10.1073/pnas.0409861102. PMC 548992. PMID 15695330.
- Liu, W.Y.; et al. (2005). "Efficient RNA interference in zebrafish embryos using synthesized with SP6 RNA polymerase". Dev Growth Differ. 47 (5): 323–31. doi:10.1111/j.1440-169x.2005.00807.x. PMID 16026540.
- Kittler, R.; et al. (2004). "An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division". Nature. 432 (7020): 1036–40. Bibcode:2004Natur.432.1036K. doi:10.1038/nature03159. PMID 15616564. S2CID 4372785.
- Yang, D.; et al. (2002). "Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells". Proc. Natl. Acad. Sci. U.S.A. 99 (15): 9942–7. Bibcode:2002PNAS...99.9942Y. doi:10.1073/pnas.152327299. PMC 126604. PMID 12096193.