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

Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal ‘short-term stress memory’ with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.

[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.