DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

(2020) Sean A. Montgomery et al.   CURRENT BIOLOGY

Polymerase IV Plays a Crucial Role in Pollen Development in Capsella

(2020) Zhenxing Wang et al.   PLANT CELL

Transposon age and non-CG methylation

(2020) Zhengming Wang et al.   Nature Communications

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

(2019) Yu Yang et al.   Journal of Integrative Plant Biology

Diversity of cytosine methylation across the fungal tree of life

(2019) Adam J. Bewick et al.   Nature Ecology & Evolution

RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs

(2019) Rafael Yaari et al.   Nature Communications

Enhancer DNA methylation: implications for gene regulation

(2019) Allegra Angeloni et al.   Essays in Biochemistry

DNA Methylation: Shared and Divergent Features across Eukaryotes

(2019) Robert J. Schmitz et al.   TRENDS IN GENETICS

Environmental and epigenetic regulation of Rider retrotransposons in tomato

(2019) Matthias Benoit et al.   PLoS Genetics

DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts

(2019) Jaemyung Choi et al.   MOLECULAR CELL

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants

(2018) Shira Corem et al.   PLANT CELL

Loss of RNA-directed DNA Methylation in Maize Chromomethylase and DDM1-type Nucleosome Remodeler Mutants

(2018) Fang-Fang Fu et al.   PLANT CELL

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

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Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways

(2018) Sarah N. Anderson et al.   G3-Genes Genomes Genetics

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

(2018) Mao-Lun Weng et al.   GENETICS

A DNA methylation reader complex that enhances gene transcription

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A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

(2017) Runxuan Zhang et al.   NUCLEIC ACIDS RESEARCH

Evolution of sequence-specific anti-silencing systems in Arabidopsis

(2017) Aoi Hosaka et al.   Nature Communications

Evolution of DNA Methylation across Insects

(2016) Adam J. Bewick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways

(2016) Feng Tan et al.   PLANT PHYSIOLOGY

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing inArabidopsis thalianaF1 epihybrids

(2016) Mélanie Rigal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comparative Analysis of 5-Azacytidine- and Zebularine-Induced DNA Demethylation

(2016) Patrick T. Griffin et al.   G3-Genes Genomes Genetics

DNA Methylation Signatures of the Plant Chromomethyltransferases

(2016) Quentin Gouil et al.   PLoS Genetics

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition

(2015) Chaoyang Cheng et al.   PLANT JOURNAL

DNA METHYLTRANSFERASE 1 is involved in mCG and mCCG DNA methylation and is essential for sporophyte development in Physcomitrella patens

(2015) Rafael Yaari et al.   PLANT MOLECULAR BIOLOGY

Methylation-Sensitive Expression of a DNA Demethylase Gene Serves As an Epigenetic Rheostat

(2015) Ben P. Williams et al.   PLoS Genetics

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

(2014) Jason T. Huff et al.   CELL

Genetic Perturbation of the Maize Methylome

(2014) Qing Li et al.   PLANT CELL

Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality

(2014) L. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation as a system of plant genomic immunity

(2014) M. Yvonne Kim et al.   TRENDS IN PLANT SCIENCE

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens

(2013) Chen Noy-Malka et al.   PLANT MOLECULAR BIOLOGY

RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1

(2013) X. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

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

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Fast gapped-read alignment with Bowtie 2

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Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

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Considering Transposable Element Diversification in De Novo Annotation Approaches

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Local DNA hypomethylation activates genes in rice endosperm

(2010) A. Zemach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

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Automated paleontology of repetitive DNA with REANNOTATE

(2008) Vini Pereira   BMC GENOMICS