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Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain

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Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain

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dc.contributor.author Gallego Bartolomé, Javier es_ES
dc.contributor.author Gardiner, Jason es_ES
dc.contributor.author Liu, Wanlu es_ES
dc.contributor.author Papikian, Ashot es_ES
dc.contributor.author Ghoshal, Basudev es_ES
dc.contributor.author Kuo, Hsuan Yu es_ES
dc.contributor.author Zhao, Jenny Miao-Chi es_ES
dc.contributor.author Segal, David J. es_ES
dc.contributor.author Jacobsen, Steven E. es_ES
dc.date.accessioned 2023-12-21T19:02:06Z
dc.date.available 2023-12-21T19:02:06Z
dc.date.issued 2018-02-27 es_ES
dc.identifier.issn 0027-8424 es_ES
dc.identifier.uri http://hdl.handle.net/10251/201047
dc.description.abstract [EN] DNA methylation is an important epigenetic modification involved in gene regulation and transposable element silencing. Changes in DNA methylation can be heritable and, thus, can lead to the formation of stable epialleles. A well-characterized example of a stable epiallele in plants is fwa, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN (FWA) gene, causing up-regulation of FWA and a heritable late-flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA up-regulation, and a heritable late-flowering phenotype. Additional ZF-TET1cd fusions designed to target methylated regions of the CACTA1 transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCas9-based targeted demethylation system using the TET1cd and a modified SunTag system. Similar to the ZF-TET1cd fusions, the SunTag-TET1cd system is able to target demethylation and activate gene expression when directed to the FWA or CACTA1 loci. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons. es_ES
dc.description.sponsorship We thank Dr. Zachary Nimchuk for the pMOA vector, and Truman Do for technical support. High-throughput sequencing was performed in the University of California, Los Angeles Broad Stem Cell Research Center BioSequencing Core Facility. This research was supported by the Bill & Melinda Gates Foundation (OPP1125410). W.L. is supported by the Philip J. Whitcome Fellowship from the University of California, Los Angeles Molecular Biology Institute and a scholarship from the Chinese Scholarship Council. D.J.S. is supported by NIH CA204563. S.E.J. is an Investigator of the Howard Hughes Medical Institute. es_ES
dc.language Inglés es_ES
dc.publisher Proceedings of the National Academy of Sciences es_ES
dc.relation.ispartof Proceedings of the National Academy of Sciences es_ES
dc.rights Reconocimiento (by) es_ES
dc.title Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1073/pnas.1716945115 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/NIH//CA204563/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/BMGF//OPP1125410/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes es_ES
dc.description.bibliographicCitation Gallego Bartolomé, J.; Gardiner, J.; Liu, W.; Papikian, A.; Ghoshal, B.; Kuo, HY.; Zhao, JM.... (2018). Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain. Proceedings of the National Academy of Sciences. 115(9):E2125-E2134. https://doi.org/10.1073/pnas.1716945115 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1073/pnas.1716945115 es_ES
dc.description.upvformatpinicio E2125 es_ES
dc.description.upvformatpfin E2134 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 115 es_ES
dc.description.issue 9 es_ES
dc.identifier.pmid 29444862 es_ES
dc.identifier.pmcid PMC5834696 es_ES
dc.relation.pasarela S\505603 es_ES
dc.contributor.funder Bill and Melinda Gates Foundation es_ES
dc.contributor.funder National Institutes of Health, EEUU es_ES
dc.description.references O Bogdanović, R Lister, DNA methylation and the preservation of cell identity. Curr Opin Genet Dev 46, 9–14 (2017). es_ES
dc.description.references T Kakutani, Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J 12, 1447–1451 (1997). es_ES
dc.description.references AA Agrawal, C Laforsch, R Tollrian, Transgenerational induction of defences in animals and plants. Nature 401, 60–63 (1999). es_ES
dc.description.references WJ Soppe, , The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6, 791–802 (2000). es_ES
dc.description.references SE Jacobsen, EM Meyerowitz, Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277, 1100–1103 (1997). es_ES
dc.description.references P Cubas, C Vincent, E Coen, An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157–161 (1999). es_ES
dc.description.references M Koornneef, CJ Hanhart, JH van der Veen, A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 229, 57–66 (1991). es_ES
dc.description.references MW Kankel, , Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163, 1109–1122 (2003). es_ES
dc.description.references JA Law, SE Jacobsen, Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11, 204–220 (2010). es_ES
dc.description.references A Zemach, , The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205 (2013). es_ES
dc.description.references L Bartee, F Malagnac, J Bender, Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev 15, 1753–1758 (2001). es_ES
dc.description.references AM Lindroth, , Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077–2080 (2001). es_ES
dc.description.references H Stroud, , Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol 21, 64–72 (2014). es_ES
dc.description.references X Cao, , Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13, 2212–2217 (2003). es_ES
dc.description.references X Cao, SE Jacobsen, Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12, 1138–1144 (2002). es_ES
dc.description.references H Stroud, MVC Greenberg, S Feng, YV Bernatavichute, SE Jacobsen, Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152, 352–364 (2013). es_ES
dc.description.references MA Matzke, T Kanno, AJM Matzke, RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants. Annu Rev Plant Biol 66, 243–267 (2015). es_ES
dc.description.references Z Gong, , ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002). es_ES
dc.description.references J Penterman, , DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104, 6752–6757 (2007). es_ES
dc.description.references J Zhu, A Kapoor, VV Sridhar, F Agius, JK Zhu, The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17, 54–59 (2007). es_ES
dc.description.references H Zhang, J-K Zhu, Active DNA demethylation in plants and animals. Cold Spring Harb Symp Quant Biol 77, 161–173 (2012). es_ES
dc.description.references T Baubec, A Pecinka, W Rozhon, O Mittelsten Scheid, Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine. Plant J 57, 542–554 (2009). es_ES
dc.description.references SM Taylor, PA Jones, Changes in phenotypic expression in embryonic and adult cells treated with 5-azacytidine. J Cell Physiol 111, 187–194 (1982). es_ES
dc.description.references PT Griffin, CE Niederhuth, RJ Schmitz, A comparative analysis of 5-azacytidine- and zebularine-induced DNA demethylation. G3 (Bethesda) 6, 2773–2780 (2016). es_ES
dc.description.references LM Johnson, , SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature 507, 124–128 (2014). es_ES
dc.description.references S Morita, , Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions. Nat Biotechnol 34, 1060–1065 (2016). es_ES
dc.description.references ML Maeder, , Targeted DNA demethylation and endogenous gene activation using programmable TALE-TET1 fusions. Nat Biotechnol 31, 1137–1142 (2013). es_ES
dc.description.references H Chen, , Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 42, 1563–1574 (2014). es_ES
dc.description.references A Amabile, , Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing. Cell 167, 219–232.e14 (2016). es_ES
dc.description.references XS Liu, , Editing DNA methylation in the mammalian genome. Cell 167, 233–247.e17 (2016). es_ES
dc.description.references X Xu, , A CRISPR-based approach for targeted DNA demethylation. Cell Discov 2, 16009 (2016). es_ES
dc.description.references SR Choudhury, Y Cui, K Lubecka, B Stefanska, J Irudayaraj, CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter. Oncotarget 7, 46545–46556 (2016). es_ES
dc.description.references M Okada, M Kanamori, K Someya, H Nakatsukasa, A Yoshimura, Stabilization of Foxp3 expression by CRISPR-dCas9-based epigenome editing in mouse primary T cells. Epigenetics Chromatin 10, 24 (2017). es_ES
dc.description.references C-L Lo, SR Choudhury, J Irudayaraj, FC Zhou, Epigenetic editing of Ascl1 gene in neural stem cells by optogenetics. Sci Rep 7, 42047 (2017). es_ES
dc.description.references X Wu, Y Zhang, TET-mediated active DNA demethylation: Mechanism, function and beyond. Nat Rev Genet 18, 517–534 (2017). es_ES
dc.description.references RM Kohli, Y Zhang, TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472–479 (2013). es_ES
dc.description.references E Hollwey, M Watson, P Meyer, Expression of the C-terminal domain of mammalian TET3 DNA dioxygenase in Arabidopsis thaliana induces heritable methylation changes at rDNA loci. Adv Biosci Biotechnol 7, 243–250 (2016). es_ES
dc.description.references ME Tanenbaum, LA Gilbert, LS Qi, JS Weissman, RD Vale, A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635–646 (2014). es_ES
dc.description.references AW Nguyen, PS Daugherty, Evolutionary optimization of fluorescent proteins for intracellular FRET. Nat Biotechnol 23, 355–360 (2005). es_ES
dc.description.references M Kato, K Takashima, T Kakutani, Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana. Genetics 168, 961–969 (2004). es_ES
dc.description.references A Miura, , Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana. Mol Genet Genomics 270, 524–532 (2004). es_ES
dc.description.references I Kardailsky, , Activation tagging of the floral inducer FT. Science 286, 1962–1965 (1999). es_ES
dc.description.references SJ Clough, AF Bent, Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16, 735–743 (1998). es_ES
dc.description.references MD Curtis, U Grossniklaus, A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133, 462–469 (2003). es_ES
dc.description.references PJ Barrell, S Yongjin, PA Cooper, AJ Conner, Alternative selectable markers for potato transformation using minimal T-DNA vectors. Plant Cell Tissue Organ Cult 70, 61–68 (2002). es_ES
dc.description.references C Trapnell, L Pachter, SL Salzberg, TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25, 1105–1111 (2009). es_ES
dc.description.references S Anders, PT Pyl, W Huber, HTSeq—A Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015). es_ES
dc.description.references Y Xi, W Li, BSMAP: Whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009). es_ES
dc.description.references SJ Cokus, , Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008). es_ES


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