Putting DNA methylation in context: from genomes to gene expression in plants (Q38945347)

13 June 2018

review article

1 reference

title

Putting DNA methylation in context: from genomes to gene expression in plants (English)

1 reference

13 June 2018

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Robert Schmitz

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

author name string

Chad E Niederhuth

series ordinal

1

1 reference

13 June 2018

Robert J Schmitz

series ordinal

2

1 reference

13 June 2018

language of work or name

English

0 references

publication date

30 August 2016

1 reference

13 June 2018

Biochimica et Biophysica Acta. Gene Regulatory Mechanisms

published in

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

volume

1860

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

page(s)

149-156

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

Widespread natural variation of DNA methylation within angiosperms

13 June 2020

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17 June 2018

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Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

17 June 2018

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Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

17 June 2018

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Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

17 June 2018

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Polyploidy and genome evolution in plants

17 June 2018

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17 June 2018

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CG gene body DNA methylation changes and evolution of duplicated genes in cassava

17 June 2018

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Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

17 June 2018

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Prediction of Plant Height in Arabidopsis thaliana Using DNA Methylation Data

17 June 2018

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Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

17 June 2018

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17 June 2018

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Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation.

17 June 2018

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Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

17 June 2018

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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

17 June 2018

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Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat

17 June 2018

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Regulatory link between DNA methylation and active demethylation in Arabidopsis

17 June 2018

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Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms

17 June 2018

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Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

17 June 2018

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Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

17 June 2018

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Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

17 June 2018

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Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization

17 June 2018

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5-hydroxymethylcytosine is not present in appreciable quantities in Arabidopsis DNA.

17 June 2018

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Epigenetic reprogramming in plant sexual reproduction.

17 June 2018

1 reference

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Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

17 June 2018

1 reference

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Pol IV-Dependent siRNA Production is Reduced in Brassica rapa

17 June 2018

1 reference

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RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

17 June 2018

1 reference

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Transgenerational epigenetic inheritance: myths and mechanisms

17 June 2018

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The contributions of transposable elements to the structure, function, and evolution of plant genomes

17 June 2018

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Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions.

17 June 2018

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Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.

17 June 2018

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The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.

17 June 2018

1 reference

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Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

17 June 2018

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Extensive natural epigenetic variation at a de novo originated gene

17 June 2018

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The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin

17 June 2018

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Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

17 June 2018

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Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

17 June 2018

1 reference

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Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

17 June 2018

1 reference

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Spreading of heterochromatin is limited to specific families of maize retrotransposons

17 June 2018

1 reference

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CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

17 June 2018

1 reference

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Loss of the DNA methyltransferase MET1 Induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana

17 June 2018

1 reference

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Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers

17 June 2018

1 reference

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'Leveling' the playing field for analyses of single-base resolution DNA methylomes.

17 June 2018

1 reference

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Birds do it, bees do it, worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life

17 June 2018

1 reference

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Deposition of histone variant H2A.Z within gene bodies regulates responsive genes

17 June 2018

1 reference

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Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

17 June 2018

1 reference

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Widespread dynamic DNA methylation in response to biotic stress

17 June 2018

1 reference

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DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns

17 June 2018

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Heritable epigenetic variation among maize inbreds

17 June 2018

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Transgenerational epigenetic instability is a source of novel methylation variants

17 June 2018

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Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

17 June 2018

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Conservation and divergence of methylation patterning in plants and animals

17 June 2018

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Genome-wide evolutionary analysis of eukaryotic DNA methylation.

17 June 2018

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Histone variants--ancient wrap artists of the epigenome

17 June 2018

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Establishing, maintaining and modifying DNA methylation patterns in plants and animals

17 June 2018

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A transposon-induced epigenetic change leads to sex determination in melon

17 June 2018

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Human DNA methylomes at base resolution show widespread epigenomic differences

17 June 2018

1 reference

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Assessing the impact of transgenerational epigenetic variation on complex traits

17 June 2018

1 reference

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Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes.

17 June 2018

1 reference

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Finding the fifth base: genome-wide sequencing of cytosine methylation.

17 June 2018

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An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.

17 June 2018

1 reference

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Epigenetic reprogramming and small RNA silencing of transposable elements in pollen

17 June 2018

1 reference

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Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves

17 June 2018

1 reference

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Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II

17 June 2018

1 reference

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DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis

17 June 2018

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Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

17 June 2018

1 reference

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Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.

17 June 2018

1 reference

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Highly integrated single-base resolution maps of the epigenome in Arabidopsis

17 June 2018

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Epigenetic interactions between transposons and genes: lessons from plants

17 June 2018

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Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

17 June 2018

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Distinctive core histone post-translational modification patterns in Arabidopsis thaliana

17 June 2018

1 reference

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Methods of DNA methylation analysis

17 June 2018

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UHRF1 plays a role in maintaining DNA methylation in mammalian cells

17 June 2018

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VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization

17 June 2018

1 reference

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Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis

17 June 2018

1 reference

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Inherited epigenetic variation--revisiting soft inheritance

17 June 2018

1 reference

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Microarray-based DNA methylation profiling: technology and applications

17 June 2018

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H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases

17 June 2018

1 reference

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Differential methylation of genes and repeats in land plants

17 June 2018

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Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes

17 June 2018

1 reference

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RNA polymerase IV directs silencing of endogenous DNA.

17 June 2018

1 reference

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Mechanisms of recent genome size variation in flowering plants

17 June 2018

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Large-scale copy number polymorphism in the human genome

17 June 2018

1 reference

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High-frequency gene transfer from the chloroplast genome to the nucleus

17 June 2018

1 reference

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Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

DNA methylation patterns and epigenetic memory

17 June 2018

1 reference

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Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

An epigenetic mutation responsible for natural variation in floral symmetry

17 June 2018

1 reference

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Arabidopsis PAI gene arrangements, cytosine methylation and expression

17 June 2018

1 reference

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A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis

17 June 2018

1 reference

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Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development

17 June 2018

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Demethylation-induced developmental pleiotropy in Arabidopsis

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Evidence for cytosine methylation of non-symmetrical sequences in transgenic Petunia hybrida

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Characterization of an Arabidopsis thaliana DNA hypomethylation mutant

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

5-Methylcytosine is not detectable in Saccharomyces cerevisiae DNA

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Inactivation of the maize transposable element Activator (Ac) is associated with its DNA modification

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

DNA modification of a maize transposable element correlates with loss of activity

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Evolutionary patterns of genic DNA methylation vary across land plants.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Genetic perturbation of the maize methylome

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Mapping the epigenetic basis of complex traits.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Patterns of population epigenomic diversity.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Recent and frequent insertions of chloroplast DNA into maize nuclear chromosomes.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Gene body DNA methylation in plants: a means to an end or an end to a means?

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

A multistep process gave rise to RNA polymerase IV of land plants.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

RNA silencing genes control de novo DNA methylation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

DNMT1 is a component of a multiprotein DNA replication complex

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Highly expressed genes in yeast evolve slowly.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Epigenetic and genetic influences on DNA methylation variation in maize populations

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203807

Molecular and genetic characterization of a novel pleiotropic tomato-ripening mutant

4 November 2018

1 reference

12 December 2020

Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase

1 reference

12 December 2020

DNA METHYLATION IN PLANTS

1 reference

12 December 2020

In plants, highly expressed genes are the least compact

1 reference

12 December 2020

Sequence specificity of methylation in higher plant DNA

1 reference

12 December 2020

Arabidopsis thaliana DNA methylation mutants

1 reference

12 December 2020

An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis

1 reference

12 December 2020

Plant cytosine-5 DNA methyltransferases: structure, function, and molecular evolution

1 reference

12 December 2020

Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases

1 reference

12 December 2020

10.1016/J.BBAGRM.2016.08.009

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27590871%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

PubMed publication ID

27590871

1 reference