Intertwined evolution of plant epigenomes and genomes

Natural variation in DNA methylation homeostasis and the emergence of epialleles

(2020) Yinwen Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

(2019) Jered M Wendte et al.   eLife

Phylogenetic shifts in gene body methylation correlate with gene expression and reflect trait conservation

(2019) Danelle K Seymour et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of DNA Methylome Diversity in Eukaryotes

(2019) Alex de Mendoza et al.   JOURNAL OF MOLECULAR BIOLOGY

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

(2019) Seydina I. Diop et al.   PLANT JOURNAL

Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation

(2019) Pierre Baduel et al.   Nature Communications

Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana

(2019) Eriko Sasaki et al.   PLoS Genetics

RNA-directed DNA Methylation and sexual reproduction: expanding beyond the seed

(2019) Hiu Tung Chow et al.   CURRENT OPINION IN PLANT BIOLOGY

Nucleosomes and DNA methylation shape meiotic DSB frequency inArabidopsis thalianatransposons and gene regulatory regions

(2018) Kyuha Choi et al.   GENOME RESEARCH

Epigenetic activation of meiotic recombination nearArabidopsis thalianacentromeres via loss of H3K9me2 and non-CG DNA methylation

(2018) Charles J. Underwood et al.   GENOME RESEARCH

Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres

(2018) Moaine El Baidouri et al.   Molecular Plant

DNA Methylation and the Evolution of Developmental Complexity in Plants

(2018) Katharina Bräutigam et al.   Frontiers in Plant Science

The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species

(2017) Shohei Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

(2016) Steven R. Eichten et al.   GENOME RESEARCH

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

DNA demethylation is initiated in the central cells ofArabidopsisand rice

(2016) Kyunghyuk Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the origin and evolutionary consequences of gene body DNA methylation

(2016) Adam J. Bewick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Methylation Signatures of the Plant Chromomethyltransferases

(2016) Quentin Gouil et al.   PLoS Genetics

Silencing of active transposable elements in plants

(2015) Dalen Fultz et al.   CURRENT OPINION IN PLANT BIOLOGY

DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination inArabidopsis

(2015) Nataliya E. Yelina et al.   GENES & DEVELOPMENT

DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination

(2015) Natasha Zamudio et al.   GENES & DEVELOPMENT

Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway

(2015) Lu Ma et al.   Genome Biology and Evolution

Ancient Origin and Recent Innovations of RNA Polymerase IV and V

(2015) Yi Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

(2015) Kyung Do Kim et al.   PLANT PHYSIOLOGY

Recombination in diverse maize is stable, predictable, and associated with genetic load

(2015) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

(2015) Qing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

(2015) Manu J Dubin et al.   eLife

Specific Modifications of Histone Tails, but Not DNA Methylation, Mirror the Temporal Variation of Mammalian Recombination Hotspots

(2014) Jia Zeng et al.   Genome Biology and Evolution

Frequent Changes in Expression Profile and Accelerated Sequence Evolution of Duplicated Imprinted Genes in Arabidopsis

(2014) Yichun Qiu et al.   Genome Biology and Evolution

Widespread and frequent horizontal transfers of transposable elements in plants

(2014) M. El Baidouri et al.   GENOME RESEARCH

Bursts of transposable elements as an evolutionary driving force

(2014) A. Belyayev   JOURNAL OF EVOLUTIONARY BIOLOGY

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

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

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

(2014) Patrick T. West et al.   PLoS One

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

(2014) Danelle K. Seymour et al.   PLoS Genetics

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

(2013) Assaf Zemach et al.   CELL

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

Transposon variation by order during allopolyploidisation betweenBrassica oleraceaandBrassica rapa

(2013) Z. An et al.   PLANT 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

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

(2013) S. Takuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin

(2013) Hidetoshi Saze et al.   Nature Communications

Epigenetic control of transposon transcription and mobility in Arabidopsis

(2012) Etienne Bucher et al.   CURRENT OPINION IN PLANT BIOLOGY

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

(2012) A. R. Leitch et al.   NEW PHYTOLOGIST

Deficiency in DNA methylation increases meiotic crossover rates in euchromatic but not in heterochromatic regions in Arabidopsis

(2012) C. Melamed-Bessudo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of DNA methylation affects the recombination landscape in Arabidopsis

(2012) M. Mirouze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) C. A. Ibarra et al.   SCIENCE

Epigenetic Remodeling of Meiotic Crossover Frequency in Arabidopsis thaliana DNA Methyltransferase Mutants

(2012) Nataliya E. Yelina et al.   PLoS Genetics

DNA Demethylation Dynamics

(2011) Nidhi Bhutani et al.   CELL

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

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novogenetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population ofBrassica napusderived from interspecific hybridization withBrassica rapa

(2011) Jun Zou et al.   PLANT JOURNAL

Heritable Epigenetic Variation among Maize Inbreds

(2011) Steve R. Eichten et al.   PLoS Genetics

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia

(2010) Ningning Wang et al.   BMC PLANT BIOLOGY

Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex

(2010) Assaf Zemach et al.   CURRENT BIOLOGY

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

DNA demethylation by DNA repair

(2009) Mary Gehring et al.   TRENDS IN GENETICS

Evolution and Control of Imprinted FWA Genes in the Genus Arabidopsis

(2008) Ryo Fujimoto et al.   PLoS Genetics