DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis

[1]  D. Hwang,et al.  CYTOKININ-RESPONSIVE GROWTH REGULATOR Regulates Cell Expansion and Cytokinin-Mediated Cell Cycle Progression. , 2021, Plant physiology.

[2]  T. Kakutani,et al.  The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W , 2021, Nature Cell Biology.

[3]  Xin Li,et al.  Salicylic Acid: Biosynthesis and Signaling. , 2021, Annual review of plant biology.

[4]  D. Zilberman,et al.  Gene body methylation mediates epigenetic inheritance of plant traits , 2021, bioRxiv.

[5]  S. Jacobsen,et al.  DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis , 2021, Proceedings of the National Academy of Sciences.

[6]  T. Halter,et al.  The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions , 2021, eLife.

[7]  N. Springer,et al.  Stories that can't be told by SNPs; DNA methylation variation in plant populations. , 2021, Current opinion in plant biology.

[8]  Huan-Wei Huang,et al.  Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance , 2020, Journal of integrative plant biology.

[9]  M. Nordborg,et al.  Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns , 2020, The EMBO journal.

[10]  T. Kyndt,et al.  Genome‐wide DNA hypomethylation shapes nematode pattern‐triggered immunity in plants , 2020, The New phytologist.

[11]  Robert J. Schmitz,et al.  Natural variation in DNA methylation homeostasis and the emergence of epialleles , 2020, Proceedings of the National Academy of Sciences.

[12]  Robert J. Schmitz,et al.  The prevalence, evolution and chromatin signatures of plant regulatory elements , 2019, Nature Plants.

[13]  D. Zilberman,et al.  DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. , 2019, Molecular cell.

[14]  J. Batley,et al.  DNA Methylation: Toward Crop Disease Resistance Improvement. , 2019, Trends in plant science.

[15]  Xin Li,et al.  Salicylic acid: biosynthesis, perception, and contributions to plant immunity. , 2019, Current opinion in plant biology.

[16]  James C. W. Locke,et al.  Widespread inter‐individual gene expression variability in Arabidopsis thaliana , 2019, Molecular systems biology.

[17]  S. Jacobsen,et al.  A DNA methylation reader complex that enhances gene transcription , 2018, Science.

[18]  L. Mao,et al.  DNA methylation dynamics during the interaction of wheat progenitor Aegilops tauschii with the obligate biotrophic fungus Blumeria graminis f. sp. tritici , 2018, The New phytologist.

[19]  Jian‐Kang Zhu,et al.  Dynamics and function of DNA methylation in plants , 2018, Nature Reviews Molecular Cell Biology.

[20]  A. Probst,et al.  Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. , 2018, The New phytologist.

[21]  Xiuren Zhang,et al.  Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression. , 2018, Developmental cell.

[22]  Barbara Kracher,et al.  The Defense Phytohormone Signaling Network Enables Rapid, High-Amplitude Transcriptional Reprogramming during Effector-Triggered Immunity[OPEN] , 2018, Plant Cell.

[23]  Thomas J. Hardcastle,et al.  Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions , 2018, Genome research.

[24]  D. Wang,et al.  A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions , 2018, Nature Communications.

[25]  D. Zilberman,et al.  DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes , 2017, eLife.

[26]  R. Weigel,et al.  A novel HER2 gene body enhancer contributes to HER2 expression , 2017, Oncogene.

[27]  Raja Jothi,et al.  Intragenic Enhancers Attenuate Host Gene Expression. , 2017, Molecular cell.

[28]  Keqiang Wu,et al.  Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis , 2017, Nature Plants.

[29]  D. Zilberman.  An evolutionary case for functional gene body methylation in plants and animals , 2017, Genome Biology.

[30]  Robert J. Schmitz,et al.  Gene body DNA methylation in plants. , 2017, Current opinion in plant biology.

[31]  Harrison W. Gabel,et al.  DNA methylation in the gene body influences MeCP2-mediated gene repression , 2016, Proceedings of the National Academy of Sciences.

[32]  Y. Saijo,et al.  Epigenetic Control of Defense Signaling and Priming in Plants , 2016, Front. Plant Sci..

[33]  A. Deleris,et al.  DNA Methylation and Demethylation in Plant Immunity. , 2016, Annual review of phytopathology.

[34]  Stefan R. Henz,et al.  Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions , 2016, Cell.

[35]  Nicolae Radu Zabet,et al.  DNA sequence properties that predict susceptibility to epiallelic switching , 2016, bioRxiv.

[36]  Philip N Benfey,et al.  Unique cell-type specific patterns of DNA methylation in the root meristem , 2016, Nature Plants.

[37]  Robert J. Schmitz,et al.  On the origin and evolutionary consequences of gene body DNA methylation , 2016, Proceedings of the National Academy of Sciences.

[38]  M. Matz,et al.  Evolutionary Consequences of DNA Methylation in a Basal Metazoan , 2016, bioRxiv.

[39]  B. Gaut,et al.  Evolutionary patterns of genic DNA methylation vary across land plants , 2016, Nature Plants.

[40]  S. Michaels,et al.  Accessing the Inaccessible: The Organization, Transcription, Replication, and Repair of Heterochromatin in Plants. , 2015, Annual review of genetics.

[41]  Christopher A. Penfold,et al.  Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000[OPEN] , 2015, Plant Cell.

[42]  Toshiro Ito,et al.  Dynamics of H3K27me3 methylation and demethylation in plant development , 2015, Plant signaling & behavior.

[43]  D. Patel,et al.  DNA methylation pathways and their crosstalk with histone methylation , 2015, Nature Reviews Molecular Cell Biology.

[44]  Ahmad Tarmizi Hashim,et al.  Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm , 2015, Nature.

[45]  Gunnar Rätsch,et al.  DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation , 2015, eLife.

[46]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[47]  Joana Sequeira-Mendes,et al.  The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States[C][W] , 2014, Plant Cell.

[48]  M. Matzke,et al.  RNA-directed DNA methylation: an epigenetic pathway of increasing complexity , 2014, Nature reviews genetics.

[49]  D. Hwang,et al.  iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis. , 2014, Molecular plant.

[50]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[51]  Christopher J. Hale,et al.  SRA/SET domain-containing proteins link RNA polymerase V occupancy to DNA methylation , 2014, Nature.

[52]  D. Patel,et al.  The roles of non-CG methylation in Arabidopsis , 2013, Nature Structural &Molecular Biology.

[53]  D. Patel,et al.  Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis , 2013, Nature Structural & Molecular Biology.

[54]  D. Coleman-Derr,et al.  The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin , 2013, Cell.

[55]  Matthew D. Schultz,et al.  Patterns of Population Epigenomic Diversity , 2013, Nature.

[56]  Daehee Hwang,et al.  A Systems Approach for Decoding Mitochondrial Retrograde Signaling Pathways , 2013, Science Signaling.

[57]  Anne-Laure Abraham,et al.  Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense , 2013, Proceedings of the National Academy of Sciences.

[58]  B. Gaut,et al.  Gene body methylation is conserved between plant orthologs and is of evolutionary consequence , 2013, Proceedings of the National Academy of Sciences.

[59]  S. Jacobsen,et al.  Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome , 2013, Cell.

[60]  Anushya Muruganujan,et al.  PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees , 2012, Nucleic Acids Res..

[61]  E. Bucher,et al.  Epigenetic control of transposon transcription and mobility in Arabidopsis. , 2012, Current opinion in plant biology.

[62]  Alfonso Valencia,et al.  Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia , 2012, Nature Genetics.

[63]  D. Coleman-Derr,et al.  Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes , 2012, PLoS genetics.

[64]  D. Patel,et al.  Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants , 2012, Cell.

[65]  B. Hunt,et al.  The evolution of invertebrate gene body methylation. , 2012, Molecular biology and evolution.

[66]  Jill M Dowen,et al.  Widespread dynamic DNA methylation in response to biotic stress , 2012, Proceedings of the National Academy of Sciences.

[67]  Peter A. Jones.  Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.

[68]  S. Jacobsen,et al.  Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana , 2012, Proceedings of the National Academy of Sciences.

[69]  E. Wagner,et al.  Understanding the language of Lys36 methylation at histone H3 , 2012, Nature Reviews Molecular Cell Biology.

[70]  Karsten M. Borgwardt,et al.  Spontaneous epigenetic variation in the Arabidopsis thaliana methylome , 2011, Nature.

[71]  R. Sandberg,et al.  CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing , 2011, Nature.

[72]  Matthew D. Schultz,et al.  Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants , 2011, Science.

[73]  W. Reik,et al.  Epigenetic Reprogramming in Plant and Animal Development , 2010, Science.

[74]  John P. Rathjen,et al.  Plant immunity: towards an integrated view of plant–pathogen interactions , 2010, Nature Reviews Genetics.

[75]  D. Zilberman,et al.  Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation , 2010, Science.

[76]  Julie A. Law,et al.  Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.

[77]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[78]  Young-Joon Kim,et al.  Nucleosome deposition and DNA methylation at coding region boundaries , 2009, Genome Biology.

[79]  A. Maldonado,et al.  Evidence for a positive regulatory role of strawberry (Fragaria x ananassa) Fa WRKY1 and Arabidopsis At WRKY75 proteins in resistance. , 2009, Journal of experimental botany.

[80]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[81]  S. Henikoff,et al.  Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks , 2008, Nature.

[82]  Felipe F. Aceituno,et al.  The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana , 2008, BMC Genomics.

[83]  I. Henderson,et al.  Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. , 2008, Genes & development.

[84]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.

[85]  S. Nelson,et al.  Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning , 2008, Nature.

[86]  K. Mitsuya,et al.  The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA , 2007, Nature.

[87]  S. Jacobsen,et al.  UHRF1 Plays a Role in Maintaining DNA Methylation in Mammalian Cells , 2007, Science.

[88]  Jonathan D. G. Jones,et al.  The plant immune system , 2006, Nature.

[89]  B. Poinssot,et al.  Priming: getting ready for battle. , 2006, Molecular plant-microbe interactions : MPMI.

[90]  S. Chisholm,et al.  Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response , 2022 .

[91]  Hamid Bolouri,et al.  A data integration methodology for systems biology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[92]  J. Ton,et al.  Dissecting the β-Aminobutyric Acid–Induced Priming Phenomenon in Arabidopsisw⃞ , 2005, The Plant Cell Online.

[93]  Mark Groudine,et al.  Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells , 2004, Nature Structural &Molecular Biology.

[94]  Xinnian Dong,et al.  NPR1, all things considered. , 2004, Current opinion in plant biology.

[95]  Jonathan D. G. Jones,et al.  Bacterial disease resistance in Arabidopsis through flagellin perception , 2004, Nature.

[96]  Jing Li,et al.  The WRKY70 Transcription Factor: A Node of Convergence for Jasmonate-Mediated and Salicylate-Mediated Signals in Plant Defense On-line version contains Web-only data. , 2004, The Plant Cell Online.

[97]  M. Campbell,et al.  PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.

[98]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[99]  F. Ausubel,et al.  MAP kinase signalling cascade in Arabidopsis innate immunity , 2002, Nature.

[100]  T. Kakutani,et al.  Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis , 2001, Nature.

[101]  J. Metraux,et al.  Potentiation of pathogen-specific defense mechanisms in Arabidopsis by beta -aminobutyric acid. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[102]  E. Selker,et al.  DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. , 1997, Genes & development.

[103]  Jane Glazebrook,et al.  The Arabidopsis NPR1 Gene That Controls Systemic Acquired Resistance Encodes a Novel Protein Containing Ankyrin Repeats , 1997, Cell.

[104]  M. McArthur,et al.  A preference of histone H1 for methylated DNA. , 1996, The EMBO journal.

[105]  Alfred V. Aho,et al.  Awk — a pattern scanning and processing language , 1979, Softw. Pract. Exp..

[106]  T. Michael,et al.  Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. , 2013, The Plant journal : for cell and molecular biology.

[107]  Aric Hagberg,et al.  Exploring Network Structure, Dynamics, and Function using NetworkX , 2008 .

[108]  J. Ton,et al.  Dissecting the b -Aminobutyric Acid–Induced Priming Phenomenon in Arabidopsis , 2005 .