Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity
暂无分享,去创建一个
Detlef Weigel | Claude Becker | Hadi Putra | D. Weigel | J. Kageyama | J. Hagmann | J. Becker | G. Marconi | J. Gutierrez-Marcos | Anjar Wibowo | Gianpiero Marconi | Julius Durr | Jonathan Price | Jorg Hagmann | Ranjith Papareddy | Jorge Kageyama | Jorg Becker | Jose Gutierrez-Marcos | A. Wibowo | Ranjith K. Papareddy | Julius Durr | Hadi Putra | Jonathan Price | C. Becker | H. Putra
[1] S. Zhong,et al. Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening , 2013, Nature Biotechnology.
[2] N. Warthmann,et al. Simultaneous alignment of short reads against multiple genomes , 2009, Genome Biology.
[3] Y. Ilnytskyy,et al. Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins , 2010, PloS one.
[4] E Nevo,et al. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[5] C. Sullivan,et al. MicroRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana[W][OA] , 2010, Plant Cell.
[6] Jian‐Kang Zhu,et al. Regulatory link between DNA methylation and active demethylation in Arabidopsis , 2015, Proceedings of the National Academy of Sciences.
[7] T. Uller,et al. When is incomplete epigenetic resetting in germ cells favoured by natural selection? , 2015, Proceedings of the Royal Society B: Biological Sciences.
[8] P. Itskov,et al. Paternal Diet Defines Offspring Chromatin State and Intergenerational Obesity , 2014, Cell.
[9] D. Baek,et al. Regulated Athkt1 Gene Expression by a Distal Enhancer Element and Dna Methylation in the Promoter Plays an Important Role in Salt Tolerance Results Identification of Sos3 Suppressors , 2022 .
[10] P. Mourrain,et al. DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis , 2000, Current Biology.
[11] Huan Wang,et al. PLncDB: plant long non-coding RNA database , 2013, Bioinform..
[12] 真田 昌. 骨髄異形成症候群のgenome-wide analysis , 2013 .
[13] U. Grossniklaus,et al. Selected aspects of transgenerational epigenetic inheritance and resetting in plants. , 2011, Current opinion in plant biology.
[14] Matthew D. Schultz,et al. Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants , 2011, Science.
[15] Sibum Sung,et al. Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA , 2011, Science.
[16] A. Schnittger,et al. Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin–Dependent Regulation of AGAMOUS-LIKE36 , 2011, PLoS genetics.
[17] E. Bucher,et al. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress , 2011, Nature.
[18] W. Scheible,et al. AtMyb41 Regulates Transcriptional and Metabolic Responses to Osmotic Stress in Arabidopsis[W][OA] , 2009, Plant Physiology.
[19] Jian‐Kang Zhu. Active DNA demethylation mediated by DNA glycosylases. , 2009, Annual review of genetics.
[20] R. Martienssen,et al. Transgenerational Epigenetic Inheritance: Myths and Mechanisms , 2014, Cell.
[21] D. Baulcombe,et al. RNA Polymerase IV Directs Silencing of Endogenous DNA , 2005, Science.
[22] C. Mello,et al. piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline , 2012, Cell.
[23] S Rozen,et al. Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.
[24] Andrew M. Simons,et al. Modes of response to environmental change and the elusive empirical evidence for bet hedging , 2011, Proceedings of the Royal Society B: Biological Sciences.
[25] U. Conrath,et al. Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response , 2011, EMBO reports.
[26] F. Ariel,et al. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. , 2014, Developmental cell.
[27] S. Henikoff,et al. Methylation-Sensitive Expression of a DNA Demethylase Gene Serves As an Epigenetic Rheostat , 2015, bioRxiv.
[28] Teddy Jégu,et al. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. , 2014, Molecular cell.
[29] J. Ton,et al. The epigenetic machinery controlling transgenerational systemic acquired resistance , 2012, Plant signaling & behavior.
[30] H. Dickinson,et al. Epigenetic reprogramming in plant reproductive lineages. , 2012, Plant & cell physiology.
[31] Kabin Xie,et al. Genome-wide prediction of highly specific guide RNA spacers for CRISPR-Cas9-mediated genome editing in model plants and major crops. , 2014, Molecular plant.
[32] Jill M Dowen,et al. Widespread dynamic DNA methylation in response to biotic stress , 2012, Proceedings of the National Academy of Sciences.
[33] A. Wolffe,et al. DNA demethylation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[34] W. Peacock,et al. DNA METHYLATION IN PLANTS. , 1998, Annual review of plant physiology and plant molecular biology.
[35] Parental effects and the evolution of phenotypic memory , 2016, Journal of evolutionary biology.
[36] W. Aufsatz,et al. Transgenerational epigenetic inheritance in plants. , 2011, Biochimica et biophysica acta.
[37] J. Hollunder,et al. The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression , 2012, PloS one.
[38] B. Gaut,et al. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. , 2009, Genome research.
[39] Steven J. M. Jones,et al. Circos: an information aesthetic for comparative genomics. , 2009, Genome research.
[40] Mathieu Blanchette,et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution , 2013, Nature Genetics.
[41] Hiroki Saito,et al. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression , 2009, Nature.
[42] M. Fraga,et al. Epigenetics and the environment: emerging patterns and implications , 2012, Nature Reviews Genetics.
[43] S. Sultan,et al. HOW STABLE ‘SHOULD’ EPIGENETIC MODIFICATIONS BE? INSIGHTS FROM ADAPTIVE PLASTICITY AND BET HEDGING , 2014, Evolution; international journal of organic evolution.
[44] S. Henikoff,et al. DNA demethylation in the Arabidopsis genome , 2007, Proceedings of the National Academy of Sciences.
[45] Adam M. Gustafson,et al. Genetic and Functional Diversification of Small RNA Pathways in Plants , 2004, PLoS biology.
[46] D. Weigel,et al. Transposon Variants and Their Effects on Gene Expression in Arabidopsis , 2013, PLoS genetics.
[47] S. Clough,et al. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.
[48] Leonard D. Goldstein,et al. piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans , 2012, Cell.
[49] D. Weigel,et al. Salinity Is an Agent of Divergent Selection Driving Local Adaptation of Arabidopsis to Coastal Habitats1[OPEN] , 2015, Plant Physiology.
[50] Richard M. Clark,et al. Sequencing of natural strains of Arabidopsis thaliana with short reads. , 2008, Genome research.
[51] Gunnar Rätsch,et al. Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. , 2009, The Plant journal : for cell and molecular biology.
[52] H. Puchta,et al. Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. , 2014, The Plant journal : for cell and molecular biology.
[53] D. Zilberman,et al. DNA methylation as a system of plant genomic immunity. , 2014, Trends in plant science.
[54] E. Bornberg-Bauer,et al. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. , 2007, The Plant journal : for cell and molecular biology.
[55] Antoine H. F. M. Peters,et al. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism , 2014, Science.
[56] A. Agrawal. Transgenerational Consequences of Plant Responses to Herbivory: An Adaptive Maternal Effect? , 2001, The American Naturalist.
[57] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[58] Masakazu Satou,et al. Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. , 2008, Plant & cell physiology.
[59] Huiming Zhang,et al. Active DNA demethylation in plants and animals. , 2012, Cold Spring Harbor symposia on quantitative biology.
[60] R. Slotkin,et al. The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs1[W][OA] , 2013, Plant Physiology.
[61] R. Martienssen,et al. Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA , 2012, Cell.
[62] S. Jacobsen,et al. Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome , 2013, Cell.
[63] A. Agrawal,et al. Herbivory in the Previous Generation Primes Plants for Enhanced Insect Resistance1[W][OA] , 2011, Plant Physiology.
[64] B. Vanyushin. DNA methylation in plants. , 2008, Current topics in microbiology and immunology.
[65] D. Zilberman,et al. Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes , 2012, Science.
[66] Nathan M. Springer,et al. Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress , 2015, Front. Plant Sci..
[67] J. Doudna,et al. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.
[68] I. Henderson,et al. RNAi, DRD1, and Histone Methylation Actively Target Developmentally Important Non-CG DNA Methylation in Arabidopsis , 2006, PLoS genetics.
[69] C. Dean,et al. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target , 2009, Nature.
[70] Alfred Pingoud,et al. Real‐Time Polymerase Chain Reaction , 2003, Chembiochem : a European journal of chemical biology.
[71] Qian-Hao Zhu,et al. DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis , 2014, Genome Biology.
[72] R. Mott,et al. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations , 2014, Genome research.
[73] Thomas D. Schmittgen,et al. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.
[74] F. Berger,et al. Epigenetic reprogramming in plant sexual reproduction , 2014, Nature Reviews Genetics.
[75] Anushya Muruganujan,et al. Large-scale gene function analysis with the PANTHER classification system , 2013, Nature Protocols.
[76] R. Martienssen,et al. Reprogramming the epigenome in Arabidopsis pollen. , 2012, Cold Spring Harbor symposia on quantitative biology.
[77] R. J. Porra,et al. The chequered history of the development and use of simultaneous equations for the accurate determination of chlorophylls a and b , 2004, Photosynthesis Research.
[78] Jian‐Kang Zhu,et al. Protocol: a beginner’s guide to the analysis of RNA-directed DNA methylation in plants , 2014, Plant Methods.
[79] Yong-guan Zhu,et al. Inositol transporters AtINT2 and AtINT4 regulate arsenic accumulation in Arabidopsis seeds , 2015, Nature Plants.
[80] Karsten M. Borgwardt,et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome , 2011, Nature.
[81] H. J. Kim,et al. An Arabidopsis R2R3‐MYB transcription factor, AtMYB20, negatively regulates type 2C serine/threonine protein phosphatases to enhance salt tolerance , 2013, FEBS letters.
[82] Nicole Lettner,et al. How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation , 2014, PLoS genetics.
[83] B. Poinssot,et al. Priming: getting ready for battle. , 2006, Molecular plant-microbe interactions : MPMI.
[84] K. Naito,et al. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice , 2013, Molecular Breeding.
[85] Guodong Yang,et al. Salt-induced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis , 2015, Journal of experimental botany.
[86] A. Hoffmann,et al. Genetics of climate change adaptation. , 2012, Annual review of genetics.
[87] O. Mittelsten Scheid,et al. Stress-Induced Chromatin Changes: A Critical View on Their Heritability , 2012, Plant & cell physiology.
[88] O. Borsani,et al. Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis , 2005, Cell.
[89] Matthew D. Schultz,et al. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements , 2015, eLife.
[90] B. Lahner,et al. Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana , 2012, PloS one.
[91] A. Moorman,et al. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data , 2003, Neuroscience Letters.
[92] K. Shinozaki,et al. CNI1/ATL31, a RING-type ubiquitin ligase that functions in the carbon/nitrogen response for growth phase transition in Arabidopsis seedlings. , 2009, The Plant journal : for cell and molecular biology.
[93] D. Weigel,et al. Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization , 2014, PLoS genetics.
[94] Karsten M. Borgwardt,et al. Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage , 2014, bioRxiv.
[95] V. Colot,et al. Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome , 2013, Genome Biology.
[96] C. Feschotte,et al. Regulatory evolution of innate immunity through co-option of endogenous retroviruses , 2016, Science.
[97] Julie A. Law,et al. Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.
[98] M. Matzke,et al. Homology-dependent gene silencing and host defense in plants. , 2002, Advances in genetics.
[99] Sudesh Kumar Yadav,et al. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. , 2010, The Plant journal : for cell and molecular biology.
[100] Cyril Zipfel,et al. Transgeneration memory of stress in plants , 2006, Nature.
[101] Diep Ganguly,et al. Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics , 2016, Science Advances.
[102] Björn Sjögreen,et al. The real-time polymerase chain reaction. , 2006, Molecular aspects of medicine.
[103] N. Chua,et al. Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis[C][W] , 2012, Plant Cell.
[104] B. Hohn,et al. Descendants of Primed Arabidopsis Plants Exhibit Resistance to Biotic Stress1[W][OA] , 2011, Plant Physiology.
[105] R. Martienssen,et al. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei , 2012, Plant Methods.
[106] Olga Popova,et al. Transgenerational Inheritance and Resetting of Stress-Induced Loss of Epigenetic Gene Silencing in Arabidopsis , 2010, Molecular plant.