Decrease in DNA methylation 1 (DDM1) is required for the formation of mCHH islands in maize

Long, Jincheng; Xia, Ai Ai; Liu, Jing Han; Jing, Ju; Wang, Yazhong; Qi, Chuang; He, Yan

doi:10.1111/jipb.12733

Cited by 36 publications

(33 citation statements)

References 61 publications

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“…Next, we set to validate the causative role of DNA methylation on gene expression by using methylome mutants. We took advantage of the RNA-seq data from kernel tissue of the ddm1 double mutant which disturbs DNA methylome dramatically [37]. We assessed whether the genes detected as exhibiting natural variation for DNA methylation linked to DMRs in our population would also show changes in expression in the ddm1 mutant.…”

Section: Resultsmentioning

confidence: 99%

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Guo

Hermanson

et al. 2019

Genome Biol

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Background: DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize. Results: We perform targeted DNA methylation profiling for a diverse panel of 263 maize inbred genotypes. All genotypes show similar levels of DNA methylation globally, highlighting the importance of DNA methylation in maize development. Nevertheless, we identify more than 16,000 differentially methylated regions (DMRs) that are distributed across the 10 maize chromosomes. Genome-wide association analysis with high-density genetic markers reveals that over 60% of the DMRs are not tagged by SNPs, suggesting the presence of unique information in DMRs. Strong associations between DMRs and the expression of many genes are identified in both the leaf and kernel tissues, pointing to the biological significance of methylation variation. Association analysis with 986 metabolic traits suggests that DNA methylation is associated with phenotypic variation of 156 traits. There are some traits that only show significant associations with DMRs and not with SNPs. Conclusions: These results suggest that DNA methylation can provide unique information to explain phenotypic variation in maize.

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Section: Resultsmentioning

confidence: 99%

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Guo

Hermanson

et al. 2019

Genome Biol

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“…Once established, CG methylation in Arabidopsis is maintained by MET1, which is homologous to mammalian DNMT1 and recognizes hemi‐methylated me CG/GC generated by DNA replication and methylates the unmodified cytosine; meanwhile, CHG methylation is maintained by the plant specific methyltransferase CMT3 or CMT2. Maintenance of the asymmetric CHH methylation in plants is achieved by constant de novo methylation, either through the RdDM pathway or through an alternative maintenance pathway that depends on the methyltransferase CMT2 and the chromatin remodeling factor DDM1 (Zemach et al ; Fu et al ; Long et al ; Tan et al ).…”

Section: Introductionmentioning

confidence: 99%

Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

Tang

Datsenka

et al. 2019

JIPB

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DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. To date, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here, we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR‐Cas9 gene editing, we generated slmet1 mutants and observed severe developmental defects with a frame‐shift mutation, including small and curly leaves, defective inflorescence, and parthenocarpy. In leaf tissues, mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole‐genome scale, leading to a disturbed transcriptome including ectopic expression of many RIN target genes such as ACC2 in leaf tissues, which are normally expressed in fruits. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture. Meanwhile, tissue culture induces non‐CG hypomethylation, which occurs more frequently at gene regions than at TE regions. Our results depict SlMET1‐ and tissue culture‐dependent tomato DNA methylomes, and that SlMET1 is required for maintaining a normal transcriptome and normal development of tomato.

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“…In addition to DNA methylation, histone posttranslational modifications (PTMs) and chromatin remodeling play vital roles in epigenetic regulation (Liu et al ): the DDM1 protein (an SNF2 family nucleosome remodeler) functions in DNA methylation regulation in all cytosine contexts (Long et al ), and the interplay between histone modification and DNA methylation is important for transcriptional regulation (Cedar and Bergman ; Saze et al ; Du et al ). The coordinated roles of the Su(var)3‐9 class of histone H3K9 methyltransferase KYP and CMT3 methyltransferase is one example of this relationship: KYP binds methylated CHG and recruits the CMT3 methyltransferase to enhance CHG methylation (Jackson et al ; Jasencakova et al ).…”

Section: Introductionmentioning

confidence: 99%

EXPORTIN 1A prevents transgene silencing in Arabidopsis by modulating nucleo‐cytoplasmic partitioning of HDA6

Zhu

Chang

et al. 2019

JIPB

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In eukaryotic cells, transport of macromolecules across the nuclear envelope is an essential process that ensures rapid exchange of cellular components, including protein and RNA molecules. Chromatin regulators involved in epigenetic control are among the molecules exported across the nuclear envelope, but the significance of this nucleo‐cytoplasmic trafficking is not well understood. Here, we use a forward screen to isolate XPO1A (a nuclear export receptor in Arabidopsis) as an anti‐silencing factor that protects transgenes from transcriptional silencing. Loss‐of‐function of XPO1A leads to locus‐specific DNA hypermethylation at transgene promoters and some endogenous loci. We found that XPO1A directly interacts with histone deacetylase HDA6 in vivo and that the xpo1a mutation causes increased nuclear retention of HDA6 protein and results in reduced histone acetylation and enhanced transgene silencing. Our results reveal a new mechanism of epigenetic regulation through the modulation of XPO1A‐dependent nucleo‐cytoplasm partitioning of a chromatin regulator.

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Decrease in DNA methylation 1 (DDM1) is required for the formation of ^mCHH islands in maize

Cited by 36 publications

References 61 publications

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

EXPORTIN 1A prevents transgene silencing in Arabidopsis by modulating nucleo‐cytoplasmic partitioning of HDA6

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