Unique cell-type-specific patterns of DNA methylation in the root meristem

Kawakatsu, Taiji; Stuart, T.A.; Valdes, Marcelo E.; Breakfield, Natalie W.; Schmitz, Robert J.; Nery, Joseph R.; Urich, Mark A.; Han, Xing; Lister, Ryan; Benfey, Philip N.; Ecker, Joseph R.

doi:10.1038/nplants.2016.58

Cited by 173 publications

(167 citation statements)

References 50 publications

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“…The comparison of the apple leaf and fruit methylomes revealed a noteworthy pattern-the fruit globally had higher CHH DNA methylation levels, which suggested increased activity of the RNA-directed DNA methylation machinery in this organ 54 . Consistent with this observation, it has been shown for Arabidopsis that cell-type-specific DNA methylation differences mainly occur at CHH sites 55 . Notably, DNA methylation differences in the CHH context between leaf and fruit tissues occurred next to 294 genes.…”

Section: Discussionsupporting

confidence: 78%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

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Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

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Section: Discussionsupporting

confidence: 78%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

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“…CMTs are dependent on H3K9me2, so it is reasonable to hypothesize that CHH and even CHG methylation in the vegetative nucleus may be largely dependent on RdDM. The columella cells in the Arabidopsis root cap also have much higher CHH methylation than neighboring cells, with elevated RdDM proposed as the cause (17). Our data do show that RdDM extends somewhat into heterochromatic TEs in vegetative cells (Fig.…”

Section: Discussionsupporting

confidence: 52%

“…Methylation heterogeneity between cell types within leaves and roots could, when averaged, create the impression of an overall lower methylation efficiency even though methylation within each cell type is as robust as in pollen. To circumvent this issue, we analyzed published methylation data from multiple purified root cell types (17). These cells show CG methylation levels comparable to those of whole roots and well below those of male reproductive cells (Fig.…”

Section: Cg Methylation Is More Robustly Maintained In Pollen Than Inmentioning

confidence: 99%

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Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues

Hsieh

Buttress

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cellsthe cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.DNA methylation | epigenetic inheritance | histone H1 | pollen C ytosine methylation is a covalent DNA modification that regulates transcription in eukaryotes (1). The highest levels of methylation in plant and animal genomes are typically located within symmetric CG dinucleotides (1). Methylation in this sequence context is virtually ubiquitous in plant transposable elements (TEs), which are transcriptionally silenced by methylation, but also occurs within many genes without disrupting their expression (1, 2). CG methylation is catalyzed by the Dnmt1 methyltransferase family, called MET1 in plants (1, 2). MET1 restores full methylation of hemimethylated CG dinucleotides generated by DNA replication, thereby perpetuating methylation patterns after cell division (1, 2). This maintenance activity is thought to allow DNA methylation to carry epigenetic information-and influence gene expression and phenotype-across generations (3, 4). The nature of this mechanism predicts that imperfect maintenance of CG methylation should lead to complete loss as methylation is diluted during each cell division, so that the only stable methylation states for a CG site in a population of cells should be fully methylated or fully unmethylated. However, the methylation levels measured at Arabidopsis thaliana CG site...

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“…Cell-line and tissue-specific DNA modifications are central features of multicellular development, and there are substantial differences in DNA methylation between different cell and tissue types in both humans and plants 19,20 . Understanding how these elements impact cellular activity is important for linking epigenetic changes with phenotypes.…”

Section: Analysis Of Dap-seq Datamentioning

confidence: 99%

Mapping genome-wide transcription-factor binding sites using DAP-seq

Bartlett¹,

O’Malley²,

Huang³

et al. 2017

Nat Protoc

446

285

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In order to enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF) binding site discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than ChIP-seq. DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell-and tissue-specific chemical modifications that are known to impact TF binding (such as DNA methylation) and providing increased specificity compared to in silico motif prediction methods such as protein binding microarrays (PBM) and systematic evolution of ligands by exponential enrichment (SELEX). The resulting DNA library is incubated with an affinity-tagged in vitro expressed TF, and TF-DNA complexes are purified using magnetic separation of the affinity tag. Bound genomic DNA is eluted from the TF and sequenced using next-generation sequencing. Sequence reads are mapped to a reference genome, identifying genome-wide binding locations for each TF assayed, from which sequence motifs can then be

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Unique cell-type-specific patterns of DNA methylation in the root meristem

Cited by 173 publications

References 50 publications

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues

Mapping genome-wide transcription-factor binding sites using DAP-seq

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