CRISPR-Induced Expression of N-Terminally Truncated Dicer in Mouse Cells

. 2021 Apr 08 ; 12 (4) : . [epub] 20210408

Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid33918028

RNA interference (RNAi) designates sequence-specific mRNA degradation mediated by small RNAs generated from long double-stranded RNA (dsRNA) by RNase III Dicer. RNAi appears inactive in mammalian cells except for mouse oocytes, where high RNAi activity exists because of an N-terminally truncated Dicer isoform, denoted DicerO. DicerO processes dsRNA into small RNAs more efficiently than the full-length Dicer expressed in somatic cells. DicerO is expressed from an oocyte-specific promoter of retrotransposon origin, which is silenced in other cell types. In this work, we evaluated CRISPR-based strategies for epigenetic targeting of the endogenous Dicer gene to restore DicerO expression and, consequently, RNAi. We show that reactivation of DicerO expression can be achieved in mouse embryonic stem cells, but it is not sufficient to establish a robust canonical RNAi response.

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Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998;391:806–811. doi: 10.1038/35888. PubMed DOI

Jinek M., Doudna J.A. A three-dimensional view of the molecular machinery of RNA interference. Nat. Cell Biol. 2008;457:405–412. doi: 10.1038/nature07755. PubMed DOI

Svoboda P. Renaissance of mammalian endogenous RNAi. FEBS Lett. 2014;588:2550–2556. doi: 10.1016/j.febslet.2014.05.030. PubMed DOI

Macrae I.J., Ma E., Zhou M., Robinson C.V., Doudna J.A. In vitro reconstitution of the human RISC-loading complex. Proc. Natl. Acad. Sci. USA. 2008;105:512–517. doi: 10.1073/pnas.0710869105. PubMed DOI PMC

Suk K., Choi J., Suzuki Y., Ozturk S.B., Mellor J.C., Wong K.H., Mackay J.L., Gregory R.I., Roth F.P. Reconstitution of human RNA interference in budding yeast. Nucleic Acids Res. 2011;39:e43. doi: 10.1093/nar/gkq1321. PubMed DOI PMC

Wang Y., Mercier R., Hobman T.C., Lapointe P. Regulation of RNA interference by Hsp90 is an evolutionarily conserved process. Biochim. Biophys. Acta (BBA) Bioenerg. 2013;1833:2673–2681. doi: 10.1016/j.bbamcr.2013.06.017. PubMed DOI

Bartel D.P. Metazoan MicroRNAs. Cell. 2018;173:20–51. doi: 10.1016/j.cell.2018.03.006. PubMed DOI PMC

Gantier M.P., Williams B.R. The response of mammalian cells to double-stranded RNA. Cytokine Growth Factor Rev. 2007;18:363–371. doi: 10.1016/j.cytogfr.2007.06.016. PubMed DOI PMC

Kennedy E.M., Whisnant A.W., Kornepati A.V.R., Marshall J.B., Bogerd H.P., Cullen B.R. Production of functional small interfering RNAs by an amino-terminal deletion mutant of human Dicer. Proc. Natl. Acad. Sci. USA. 2015;112:E6945–E6954. doi: 10.1073/pnas.1513421112. PubMed DOI PMC

Maillard P.V., Van Der Veen A.G., Deddouche-Grass S., Rogers N.C., Merits A., Sousa C.R.E. Inactivation of the type I interferon pathway reveals long double-stranded RNA -mediated RNA interference in mammalian cells. EMBO J. 2016;35:2505–2518. doi: 10.15252/embj.201695086. PubMed DOI PMC

Van Der Veen A.G., Maillard P.V., Schmidt J.M., Lee A.S., Deddouche-Grass S., Borg A., Kjær S., Snijders A.P., Sousa C.R.E. The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells. EMBO J. 2018;37:e97479. doi: 10.15252/embj.201797479. PubMed DOI PMC

Demeter T., Vaskovicova M., Malik R., Horvat F., Pasulka J., Svobodova E., Flemr M., Svoboda P. Main constraints for RNAi induced by expressed long dsRNA in mouse cells. Life Sci. Alliance. 2019;2:e201800289. doi: 10.26508/lsa.201800289. PubMed DOI PMC

Ma E., Macrae I.J., Kirsch J.F., Doudna J.A. Autoinhibition of human dicer by its internal helicase domain. J. Mol. Biol. 2008;380:237–243. doi: 10.1016/j.jmb.2008.05.005. PubMed DOI PMC

Flemr M., Malik R., Franke V., Nejepinska J., Sedlacek R., Vlahovicek K., Svoboda P. A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell. 2013;155:807–816. doi: 10.1016/j.cell.2013.10.001. PubMed DOI

Franke V., Ganesh S., Karlic R., Malik R., Pasulka J., Horvat F., Kuzman M., Fulka H., Cernohorska M., Urbanova J., et al. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res. 2017;27:1384–1394. doi: 10.1101/gr.216150.116. PubMed DOI PMC

Carroll D. Genome engineering with targetable nucleases. Annu. Rev. Biochem. 2014;83:409–439. doi: 10.1146/annurev-biochem-060713-035418. PubMed DOI

Beerli R.R., Segal D.J., Dreier B., Barbas C.F. Toward controlling gene expression at will: Specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. Proc. Natl. Acad. Sci. USA. 1998;95:14628–14633. doi: 10.1073/pnas.95.25.14628. PubMed DOI PMC

Zhang F., Cong L., Lodato S., Kosuri S., Church G.M., Arlotta P. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol. 2011;29:149–153. doi: 10.1038/nbt.1775. PubMed DOI PMC

Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337:816–821. doi: 10.1126/science.1225829. PubMed DOI PMC

Gilbert L.A., Larson M.H., Morsut L., Liu Z., Brar G.A., Torres S.E., Stern-Ginossar N., Brandman O., Whitehead E.H., Doudna J.A., et al. CRISPR-Mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154:442–451. doi: 10.1016/j.cell.2013.06.044. PubMed DOI PMC

Maeder M.L., Linder S.J., Cascio V.M., Fu Y., Ho Q.H., Joung J.K. CRISPR RNA–guided activation of endogenous human genes. Nat. Methods. 2013;10:977–979. doi: 10.1038/nmeth.2598. PubMed DOI PMC

Hilton I.B., D’Ippolito A.M., Vockley C.M., Thakore P.I., Crawford G.E., Reddy T.E., Gersbach C.A. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 2015;33:510–517. doi: 10.1038/nbt.3199. PubMed DOI PMC

Konermann S., Brigham M.D., Trevino A.E., Joung J., Abudayyeh O.O., Barcena C., Hsu P.D., Habib N., Gootenberg J.S., Nishimasu H., et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nat. Cell Biol. 2015;517:583–588. doi: 10.1038/nature14136. PubMed DOI PMC

Peabody D.S., Ely K.R. Control of translational repression by protein-protein interactions. Nucleic Acids Res. 1992;20:1649–1655. doi: 10.1093/nar/20.7.1649. PubMed DOI PMC

Huggins C.J., Malik R., Lee S., Salotti J., Thomas S., Martin N., Quiñones O.A., Alvord W.G., Olanich M.E., Keller J.R., et al. C/EBPγ Suppresses senescence and inflammatory gene expression by heterodimerizing with C/EBPβ. Mol. Cell Biol. 2013;33:3242–3258. doi: 10.1128/MCB.01674-12. PubMed DOI PMC

Hampf M., Gossen M. A protocol for combined Photinus and Renilla luciferase quantification compatible with protein assays. Anal. Biochem. 2006;356:94–99. doi: 10.1016/j.ab.2006.04.046. PubMed DOI

Sinkkonen L., Hugenschmidt T., Filipowicz W., Svoboda P. Dicer is associated with ribosomal DNA chromatin in mammalian cells. PLoS ONE. 2010;5:e12175. doi: 10.1371/journal.pone.0012175. PubMed DOI PMC

Pfaffl M.W., Horgan G.W., Dempfle L. Relative expression software tool (REST(C)) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res. 2002;30:e36. doi: 10.1093/nar/30.9.e36. PubMed DOI PMC

Weber M., Hellmann I., Stadler M.B., Ramos L., Pääbo S., Rebhan M., Schübeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 2007;39:457–466. doi: 10.1038/ng1990. PubMed DOI

Todaro G.J., Green H. Quantitative studies of the growth of mouse embryo cells in culture and their development into established lines. J. Cell Biol. 1963;17:299–313. doi: 10.1083/jcb.17.2.299. PubMed DOI PMC

A Martens J.H., O’Sullivan R.J., Braunschweig U., Opravil S., Radolf M., Steinlein P., Jenuwein T. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 2005;24:800–812. doi: 10.1038/sj.emboj.7600545. PubMed DOI PMC

Efroni S., Duttagupta R., Cheng J., Dehghani H., Hoeppner D.J., Dash C., Bazett-Jones D.P., Le Grice S., McKay R.D., Buetow K.H., et al. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell. 2008;2:437–447. doi: 10.1016/j.stem.2008.03.021. PubMed DOI PMC

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