Unknown,Transcriptomics,Genomics,Proteomics

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Widespread Dynamic DNA Methylation in Response to Biotic Stress

ABSTRACT: Regulation of gene expression by DNA methylation is crucial for defining cellular identities and coordinating organism-wide developmental programs in many organisms. In plants, modulation of DNA methylation in response to environmental conditions represents a potentially robust mechanism to regulate gene expression networks, however, examples of dynamic DNA methylation are largely limited to gene imprinting. We discovered an unexpected role for DNA methylation in regulation of the Arabidopsis thaliana immune system. Profiling the DNA methylomes of plants exposed to bacterial pathogen, avirulent bacteria, or salicylic acid (SA) hormone revealed numerous stress-induced differentially methylated regions (DMRs), many of which were intimately associated with differentially expressed genes. In response to SA, transposon-associated DMRs, which were accompanied by up-regulation of 21-nucleotide small interfering RNAs, were often coupled to transcriptional changes of the transposon or proximal genes. Thus, dynamic DNA methylation within repetitive sequences or transposons can regulate nearby genes in response to salicylic acid stress.

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Joseph Ecker

PROVIDER: E-MTAB-4226 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Widespread dynamic DNA methylation in response to biotic stress.

Dowen Robert H RH Pelizzola Mattia M Schmitz Robert J RJ Lister Ryan R Dowen Jill M JM Nery Joseph R JR Dixon Jack E JE Ecker Joseph R JR

Proceedings of the National Academy of Sciences of the United States of America 20120625 32

Regulation of gene expression by DNA methylation is crucial for defining cellular identities and coordinating organism-wide developmental programs in many organisms. In plants, modulation of DNA methylation in response to environmental conditions represents a potentially robust mechanism to regulate gene expression networks; however, examples of dynamic DNA methylation are largely limited to gene imprinting. Here we report an unexpected role for DNA methylation in regulation of the Arabidopsis t ...[more]

PMID: 22733782

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Project description:To further our understanding of the role of DNA methylation in development, Methylated DNA Immunoprecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis. Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). Almost 5,000 adult T-DMRs and 10,000 DS-DMRs were identified. Surprisingly, almost all DS-DMRs were tissue specific (i.e., methylated and ummenthylated in one or more non-overlapping tissues), indicating that the vast majority of unique sequence DNA methylation has tissue specificity. Also, many DS-DMRs were methylated at early development stages (E15 and NB) but unmethylated in adult, indicating “demethylation” has a prominent role in tissue differentiation. The pattern of DNA methylation in adult testis was dramatically different from somatic tissues in many aspects, mostly notably with a very strong bias of methylation in non-CpGi (CpG island) promoter regions (94%). Although the majority of T-DMRs and DS-DMRs tended to be in non-CpGi promoter regions, a relatively large number were also located in CpGi in promoter, intra-genic and inter-genic regions (>15% of all CpGi). Gene Ontology analysis of genes with methylation in non-CpGi promoters indicates enrichment of genes related to membrane proteins and G-protein coupled receptors. Our data also suggest regulatory roles of DNA methylation outside of promoter regions and in alternative promoter selection. Overall, our studies indicate that change in DNA methylation during development is a dynamic, widespread and tissue-specific process involving both DNA methylation and demethylation. Comparison of DNA methylation across 3 developmental stages (15 day embryo, newborn, and adult) for four tissues (brain, heart, liver and testis)

Dataset Information

Widespread Dynamic DNA Methylation in Response to Biotic Stress

Publications

Widespread dynamic DNA methylation in response to biotic stress.

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