CRISPR-based tools for targeted transcriptional and epigenetic regulation in plants
Autoři:
Joanne E. Lee aff001; Manuela Neumann aff002; Daniel Iglesias Duro aff001; Markus Schmid aff001
Působiště autorů:
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
aff001; Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tübingen, Germany
aff002; Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, People’s Republic of China
aff003
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222778
Souhrn
Programmable gene regulators that can modulate the activity of selected targets in trans are a useful tool for probing and manipulating gene function. CRISPR technology provides a convenient method for gene targeting that can also be adapted for multiplexing and other modifications to enable strong regulation by a range of different effectors. We generated a vector toolbox for CRISPR/dCas9-based targeted gene regulation in plants, modified with the previously described MS2 system to amplify the strength of regulation, and using Golden Gate-based cloning to enable rapid vector assembly with a high degree of flexibility in the choice of promoters, effectors and targets. We tested the system using the floral regulator FLOWERING LOCUS T (FT) as a target and a range of different effector domains including the transcriptional activator VP64, the H3K27 acetyltransferase p300 and the H3K9 methyltransferase KRYPTONITE. When transformed into Arabidopsis thaliana, several of the constructs caused altered flowering time phenotypes that were associated with changes in FT expression and/or epigenetic status, thus demonstrating the effectiveness of the system. The MS2-CRISPR/dCas9 system can be used to modulate transcriptional activity and epigenetic status of specific target genes in plants, and provides a versatile tool that can easily be used with different targets and types of regulation for a range of applications.
Klíčová slova:
Arabidopsis thaliana – Epigenetics – Flowering plants – Gene regulation – Genetically modified plants – Histones – Regulator genes
Zdroje
1. Piatek A, Mahfouz MM. Targeted genome regulation via synthetic programmable transcriptional regulators. Crit Rev Biotech. 2017;37(4):429–40. doi: 10.3109/07388551.2016.1165180 27093352
2. Köferle A, Stricker SH, Beck S. Brave new epigenomes: the dawn of epigenetic engineering. Genome Med. 2015;7(1):59. doi: 10.1186/s13073-015-0185-8 PMC4472160. 26089986
3. Dominguez AA, Lim WA, Qi LS. Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation. Nature Rev Mol Cell Biol. 2015;17:5. doi: 10.1038/nrm.2015.2 26670017
4. Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature. 2015;517(7536):583–8. doi: 10.1038/nature14136 25494202
5. Lowder LG, Zhou J, Zhang Y, Malzahn A, Zhong Z, Hsieh T-F, et al. Robust transcriptional activation in plants using multiplexed CRISPR-Act2.0 and mTALE-Act systems. Mol Plant. 2018;11(2):245–56. doi: 10.1016/j.molp.2017.11.010 29197638
6. Li Z, Zhang D, Xiong X, Yan B, Xie W, Sheen J, et al. A potent Cas9-derived gene activator for plant and mammalian cells. Nat Plants. 2017;3(12):930–6. Epub 2017/11/22. doi: 10.1038/s41477-017-0046-0 29158545
7. Lampropoulos A, Sutikovic Z, Wenzl C, Maegele I, Lohmann JU, Forner J. GreenGate—a novel, versatile, and efficient cloning system for plant transgenesis. PLoS ONE. 2013;8(12):e83043. doi: 10.1371/journal.pone.0083043 24376629
8. Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLOS ONE. 2008;3(11):e3647. doi: 10.1371/journal.pone.0003647 18985154
9. Turck F, Fornara F, Coupland G. Regulation and identity of florigen: FLOWERING LOCUS T moves center stage. Annu Rev Plant Biol. 2008;59(1):573–94. doi: 10.1146/annurev.arplant.59.032607.092755 18444908
10. Imlau A, Truernit E, Sauer N. Cell-to-cell and long-distance trafficking of the green fluorescent protein in the phloem and symplastic unloading of the protein into sink tissues. Plant Cell. 1999;11(3):309–22. doi: 10.1105/tpc.11.3.309 10072393
11. Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, et al. Activation Tagging of the Floral Inducer FT. Science. 1999;286(5446):1962–5. doi: 10.1126/science.286.5446.1962 10583961
12. Hiratsu K, Matsui K, Koyama T, Ohme-Takagi M. Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. Plant J. 2003;34(5):733–9. doi: 10.1046/j.1365-313x.2003.01759.x 12787253
13. Ogryzko VV, Schiltz RL, Russanova V, Howard BH, Nakatani Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell. 1996;87(5):953–9. doi: 10.1016/s0092-8674(00)82001-2 8945521
14. Tachibana M, Sugimoto K, Fukushima T, Shinkai Y. SET domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem. 2001;276(27):25309–17. doi: 10.1074/jbc.M101914200 11316813
15. Jackson JP, Lindroth AM, Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature. 2002;416(6880):556–60. doi: 10.1038/nature731 11898023
16. Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotech. 2015;33(5):510–7. doi: 10.1038/nbt.3199 25849900
17. Agne M, Blank I, Emhardt AJ, Gäbelein CG, Gawlas F, Gillich N, et al. Modularized CRISPR/dCas9 effector toolkit for target-specific gene regulation. ACS Synth Biol. 2014;3(12):986–9. doi: 10.1021/sb500035y 25524106
18. O’Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, et al. dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nuc Acids Res. 2017;45(17):9901–16. doi: 10.1093/nar/gkx578 28973434
19. Konermann S, Brigham MD, Trevino A, Hsu PD, Heidenreich M, Le C, et al. Optical control of mammalian endogenous transcription and epigenetic states. Nature. 2013;500(7463):472–6. doi: 10.1038/nature12466 23877069
20. An H, Roussot C, Suárez-López P, Corbesier L, Vincent C, Piñeiro M, et al. CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development. 2004;131(15):3615–26. doi: 10.1242/dev.01231 15229176
21. Grbic B, Bleecker AB. An altered body plan is conferred on Arabidopsis plants carrying dominant alleles of two genes. Development. 1996;122(8):2395–403. 8756285
22. Chou M-L, Yang C-H. FLD interacts with genes that affect different developmental phase transitions to regulate Arabidopsis shoot development. Plant J. 1998;15(2):231–42. doi: 10.1046/j.1365-313x.1998.00204.x 9721681
23. Ratcliffe OJ, Amaya I, Vincent CA, Rothstein S, Carpenter R, Coen ES, et al. A common mechanism controls the life cycle and architecture of plants. Development. 1998;125(9):1609–15. 9521899
24. Proveniers M, Rutjens B, Brand M, Smeekens S. The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC. Plant J. 2007;52(5):899–913. doi: 10.1111/j.1365-313X.2007.03285.x 17908157
25. Melzer S, Lens F, Gennen J, Vanneste S, Rohde A, Beeckman T. Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana. Nature Genet. 2008;40:1489. doi: 10.1038/ng.253 18997783
26. Mitsuda N, Hiratsu K, Todaka D, Nakashima K, Yamaguchi-Shinozaki K, Ohme-Takagi M. Efficient production of male and female sterile plants by expression of a chimeric repressor in Arabidopsis and rice. Plant Biotech J. 2006;4(3):325–32. doi: 10.1111/j.1467-7652.2006.00184.x 17147638
27. Heyl A, Ramireddy E, Brenner WG, Riefler M, Allemeersch J, Schmülling T. The transcriptional repressor ARR1-SRDX suppresses pleiotropic cytokinin activities in Arabidopsis. Plant Physiol. 2008;147(3):1380–95. doi: 10.1104/pp.107.115436 18502977
28. Hanano S, Goto K. Arabidopsis TERMINAL FLOWER1 is involved in the regulation of flowering time and inflorescence development through transcriptional repression. Plant Cell. 2011;23(9):3172–84. doi: 10.1105/tpc.111.088641 21890645
29. Mahfouz MM, Li L, Piatek M, Fang X, Mansour H, Bangarusamy DK, et al. Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein. Plant Mol Biol. 2012;78(3):311–21. doi: 10.1007/s11103-011-9866-x 22167390
30. Lowder LG, Zhang D, Baltes NJ, Paul JW, Tang X, Zheng X, et al. A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol. 2015;169(2):971–85. doi: 10.1104/pp.15.00636 26297141
31. Blázquez MA, Ahn JH, Weigel D. A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nature Genet. 2003;33(2):168–71. doi: 10.1038/ng1085 12548286
32. You Y, Sawikowska A, Lee JE, Benstein RM, Neumann M, Krajewski P, et al. Phloem companion cell-specific transcriptomic and epigenomic analyses identify MRF1, a regulator of flowering. Plant Cell. 2019;31(2):325–45. doi: 10.1105/tpc.17.00714 30670485
33. Jeong HJ, Yang J, Yi J, An G. Controlling flowering time by histone methylation and acetylation in arabidopsis and rice. J Plant Biol. 2015;58(4):203–10. doi: 10.1007/s12374-015-0219-1
34. Gallego-Bartolomé J, Gardiner J, Liu W, Papikian A, Ghoshal B, Kuo HY, et al. Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain. Proc Nat Acad Sci U S A. 2018;115(9):E2125–E34. doi: 10.1073/pnas.1716945115 29444862
35. Papikian A, Liu W, Gallego-Bartolomé J, Jacobsen SE. Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems. Nature Commun. 2019;10(1):729. doi: 10.1038/s41467-019-08736-7 30760722
36. Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A, Al-Shareef S, et al. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotech J. 2015;13(4):578–89. doi: 10.1111/pbi.12284 25400128
37. Park J-J, Dempewolf E, Zhang W, Wang Z-Y. RNA-guided transcriptional activation via CRISPR/dCas9 mimics overexpression phenotypes in Arabidopsis. PLOS ONE. 2017;12(6):e0179410. doi: 10.1371/journal.pone.0179410 28622347
38. Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, Voytas DF, et al. A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants. 2017;3:17018. doi: 10.1038/nplants.2017.18 28211909
39. Nissim L, Perli Samuel D, Fridkin A, Perez-Pinera P, Lu Timothy K. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell. 2014;54(4):698–710. doi: 10.1016/j.molcel.2014.04.022 24837679
40. Xie K, Minkenberg B, Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Nat Acad Sci U S A. 2015;112(11):3570–5. doi: 10.1073/pnas.1420294112 25733849
41. Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature. 2018;556:57. doi: 10.1038/nature26155 29512652
42. Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, et al. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science. 2018;361(6408):1259–62. doi: 10.1126/science.aas9129 30166441
43. Capovilla G, Symeonidi E, Wu R, Schmid M. Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana. J Exp Bot. 2017;68(18):5117–27. doi: 10.1093/jxb/erx328 29036339
44. Hellens RP, Edwards EA, Leyland NR, Bean S, Mullineaux PM. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation. Plant Mol Biol. 2000;42(6):819–32. doi: 10.1023/a:1006496308160 10890530
45. Yoo SK, Chung KS, Kim J, Lee JH, Hong SM, Yoo SJ, et al. CONSTANS activates SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 through FLOWERING LOCUS T to promote flowering in Arabidopsis. Plant Physio. 2005;139(2):770–8. doi: 10.1104/pp.105.066928 16183837
46. Clough SJ, Bent AF. Floral dip: a simplified method for Agrobacterium -mediated transformation of Arabidopsis thaliana. Plant J. 1998;16(6):735–43. doi: 10.1046/j.1365-313x.1998.00343.x 10069079
47. Spitzer M, Wildenhain J, Rappsilber J, Tyers M. BoxPlotR: a web tool for generation of box plots. Nat Methods. 2014;11(2):121–2. doi: 10.1038/nmeth.2811 24481215
48. Collani S, Neumann M, Yant L, Schmid M. FT modulates genome-wide DNA-binding of the bZIP transcription factor FD. Plant Physiol. 2019:pp.01505.2018. doi: 10.1104/pp.18.01505 30770462
49. Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature. 2004;427:164. doi: 10.1038/nature02269 14712277
50. Benhamed M, Bertrand C, Servet C, Zhou D-X. Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell. 2006;18(11):2893–903. doi: 10.1105/tpc.106.043489 17085686
Článek vyšel v časopise
PLOS One
2019 Číslo 9
- S diagnostikou Parkinsonovy nemoci může nově pomoci AI nástroj pro hodnocení mrkacího reflexu
- Je libo čepici místo mozkového implantátu?
- Pomůže v budoucnu s triáží na pohotovostech umělá inteligence?
- AI může chirurgům poskytnout cenná data i zpětnou vazbu v reálném čase
- Nová metoda odlišení nádorové tkáně může zpřesnit resekci glioblastomů
Nejčtenější v tomto čísle
- Graviola (Annona muricata) attenuates behavioural alterations and testicular oxidative stress induced by streptozotocin in diabetic rats
- CH(II), a cerebroprotein hydrolysate, exhibits potential neuro-protective effect on Alzheimer’s disease
- Comparison between Aptima Assays (Hologic) and the Allplex STI Essential Assay (Seegene) for the diagnosis of Sexually transmitted infections
- Assessment of glucose-6-phosphate dehydrogenase activity using CareStart G6PD rapid diagnostic test and associated genetic variants in Plasmodium vivax malaria endemic setting in Mauritania
Zvyšte si kvalifikaci online z pohodlí domova
Všechny kurzy