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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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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

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Título: Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain
Autor: Gallego Bartolomé, Javier Gardiner, Jason Liu, Wanlu Papikian, Ashot Ghoshal, Basudev Kuo, Hsuan Yu Zhao, Jenny Miao-Chi Segal, David J. Jacobsen, Steven E.
Entidad UPV: 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
Fecha difusión:
Resumen:
[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 ...[+]
Derechos de uso: Reconocimiento (by)
Fuente:
Proceedings of the National Academy of Sciences. (issn: 0027-8424 )
DOI: 10.1073/pnas.1716945115
Editorial:
Proceedings of the National Academy of Sciences
Versión del editor: https://doi.org/10.1073/pnas.1716945115
Código del Proyecto:
info:eu-repo/grantAgreement/NIH//CA204563/
info:eu-repo/grantAgreement/BMGF//OPP1125410/
Agradecimientos:
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 ...[+]
Tipo: Artículo

References

O Bogdanović, R Lister, DNA methylation and the preservation of cell identity. Curr Opin Genet Dev 46, 9–14 (2017).

T Kakutani, Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J 12, 1447–1451 (1997).

AA Agrawal, C Laforsch, R Tollrian, Transgenerational induction of defences in animals and plants. Nature 401, 60–63 (1999). [+]
O Bogdanović, R Lister, DNA methylation and the preservation of cell identity. Curr Opin Genet Dev 46, 9–14 (2017).

T Kakutani, Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J 12, 1447–1451 (1997).

AA Agrawal, C Laforsch, R Tollrian, Transgenerational induction of defences in animals and plants. Nature 401, 60–63 (1999).

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).

SE Jacobsen, EM Meyerowitz, Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277, 1100–1103 (1997).

P Cubas, C Vincent, E Coen, An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157–161 (1999).

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).

MW Kankel, , Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163, 1109–1122 (2003).

JA Law, SE Jacobsen, Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11, 204–220 (2010).

A Zemach, , The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205 (2013).

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).

AM Lindroth, , Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077–2080 (2001).

H Stroud, , Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol 21, 64–72 (2014).

X Cao, , Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13, 2212–2217 (2003).

X Cao, SE Jacobsen, Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12, 1138–1144 (2002).

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).

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).

Z Gong, , ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002).

J Penterman, , DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104, 6752–6757 (2007).

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).

H Zhang, J-K Zhu, Active DNA demethylation in plants and animals. Cold Spring Harb Symp Quant Biol 77, 161–173 (2012).

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).

SM Taylor, PA Jones, Changes in phenotypic expression in embryonic and adult cells treated with 5-azacytidine. J Cell Physiol 111, 187–194 (1982).

PT Griffin, CE Niederhuth, RJ Schmitz, A comparative analysis of 5-azacytidine- and zebularine-induced DNA demethylation. G3 (Bethesda) 6, 2773–2780 (2016).

LM Johnson, , SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature 507, 124–128 (2014).

S Morita, , Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions. Nat Biotechnol 34, 1060–1065 (2016).

ML Maeder, , Targeted DNA demethylation and endogenous gene activation using programmable TALE-TET1 fusions. Nat Biotechnol 31, 1137–1142 (2013).

H Chen, , Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 42, 1563–1574 (2014).

A Amabile, , Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing. Cell 167, 219–232.e14 (2016).

XS Liu, , Editing DNA methylation in the mammalian genome. Cell 167, 233–247.e17 (2016).

X Xu, , A CRISPR-based approach for targeted DNA demethylation. Cell Discov 2, 16009 (2016).

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).

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).

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).

X Wu, Y Zhang, TET-mediated active DNA demethylation: Mechanism, function and beyond. Nat Rev Genet 18, 517–534 (2017).

RM Kohli, Y Zhang, TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472–479 (2013).

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).

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).

AW Nguyen, PS Daugherty, Evolutionary optimization of fluorescent proteins for intracellular FRET. Nat Biotechnol 23, 355–360 (2005).

M Kato, K Takashima, T Kakutani, Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana. Genetics 168, 961–969 (2004).

A Miura, , Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana. Mol Genet Genomics 270, 524–532 (2004).

I Kardailsky, , Activation tagging of the floral inducer FT. Science 286, 1962–1965 (1999).

SJ Clough, AF Bent, Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16, 735–743 (1998).

MD Curtis, U Grossniklaus, A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133, 462–469 (2003).

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).

C Trapnell, L Pachter, SL Salzberg, TopHat: Discovering splice junctions with RNA-seq. Bioinformatics 25, 1105–1111 (2009).

S Anders, PT Pyl, W Huber, HTSeq—A Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

Y Xi, W Li, BSMAP: Whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009).

SJ Cokus, , Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).

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