Insights into Epigenome Evolution from Animal and Plant Methylomes

Evolution of the sperm methylome of primates is associated with retrotransposon insertions and genome instability

(2017) Kei Fukuda et al.   HUMAN MOLECULAR GENETICS

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

The sources of adaptive variation

(2017) Deborah Charlesworth et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells

(2017) Yuta Takahashi et al.   SCIENCE

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Gene and transposable element methylation in great tit (Parus major) brain and blood

(2016) Martijn F. L. Derks et al.   BMC GENOMICS

Portraits of TET-mediated DNA hydroxymethylation in cancer

(2016) Jana Jeschke et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

(2016) Isabel Mendizabal et al.   MOLECULAR BIOLOGY AND EVOLUTION

The multivariate association between genomewide DNA methylation and climate across the range ofArabidopsis thaliana

(2016) Thomas E. Keller et al.   MOLECULAR ECOLOGY

Genetic sources of population epigenomic variation

(2016) Aaron Taudt et al.   NATURE REVIEWS GENETICS

Transcription factors as readers and effectors of DNA methylation

(2016) Heng Zhu et al.   NATURE REVIEWS GENETICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

(2016) Hannah K. Long et al.   NUCLEIC ACIDS RESEARCH

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

Evolution of Epigenetic Regulation in Vertebrate Genomes

(2016) Rebecca F. Lowdon et al.   TRENDS IN GENETICS

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

(2016) Matthew Huska et al.   PLoS Computational Biology

The Epigenomic Landscape of Prokaryotes

(2016) Matthew J. Blow et al.   PLoS Genetics

CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon

(2016) Kyria Roessler et al.   PLoS One

Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq

(2015) Jinxiu Li et al.   BMC GENOMICS

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

Regulation ofHoxorthologues in the oysterCrassostrea gigasevidences a functional role for promoter DNA methylation in an invertebrate

(2015) Emma Saint-Carlier et al.   FEBS LETTERS

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation

(2015) Isabel Mendizabal et al.   HUMAN MOLECULAR GENETICS

DNA Methylation in Basal Metazoans: Insights from Ctenophores

(2015) Emily C. Dabe et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate–Vertebrate Boundary

(2015) Thomas E. Keller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci

(2015) Eilis Hannon et al.   NATURE NEUROSCIENCE

The interplay between DNA methylation and sequence divergence in recent human evolution

(2015) Irene Hernando-Herraez et al.   NUCLEIC ACIDS RESEARCH

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

(2015) Adriaan van der Graaf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The epigenomic landscape of African rainforest hunter-gatherers and farmers

(2015) Maud Fagny et al.   Nature Communications

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

(2015) Jörg Hagmann et al.   PLoS Genetics

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

(2015) Florent Lassalle 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

Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006

(2015) Matthew Ouellette et al.   Frontiers in Microbiology

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

(2015) Conchita Alonso et al.   Frontiers in Genetics

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

(2014) Edith Heard et al.   CELL

Fundamental diversity of human CpG islands at multiple biological levels

(2014) Jia Zeng et al.   Epigenetics

Purifying Selection, Drift, and Reversible Mutation with Arbitrarily High Mutation Rates

(2014) Brian Charlesworth et al.   GENETICS

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes

(2014) Dimos Gaidatzis 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

Synthetic CpG islands reveal DNA sequence determinants of chromatin structure

(2014) Elisabeth Wachter et al.   eLife

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

(2014) Arnaud R Krebs et al.   eLife

Contribution of genetic variation to transgenerational inheritance of DNA methylation

(2014) Allan F McRae et al.   GENOME BIOLOGY

Patterning and Regulatory Associations of DNA Methylation Are Mirrored by Histone Modifications in Insects

(2013) Brendan G. Hunt et al.   Genome Biology and Evolution

Age-associated epigenetic drift: implications, and a case of epigenetic thrift?

(2013) A. E. Teschendorff et al.   HUMAN MOLECULAR GENETICS

The Function of Intragenic DNA Methylation: Insights from Insect Epigenomes

(2013) B. G. Hunt et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

(2013) S. R. Eichten et al.   PLANT CELL

Transgenerational Variations in DNA Methylation Induced by Drought Stress in Two Rice Varieties with Distinguished Difference to Drought Resistance

(2013) Xiaoguo Zheng et al.   PLoS One

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

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc

(2013) Mackenzie R. Gavery et al.   PeerJ

Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution

(2012) Jia Zeng et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

(2012) Eugénie Pessia et al.   Genome Biology and Evolution

The Evolution of Invertebrate Gene Body Methylation

(2012) S. Sarda et al.   MOLECULAR BIOLOGY AND EVOLUTION

Understanding transgenerational epigenetic inheritance via the gametes in mammals

(2012) Lucia Daxinger et al.   NATURE REVIEWS GENETICS

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The correlation of genome size and DNA methylation rate in metazoans

(2012) Marcus Lechner et al.   THEORY IN BIOSCIENCES

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

(2012) Jordana T. Bell et al.   PLoS Genetics

Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection

(2011) Netta Mendelson Cohen et al.   CELL

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

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

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

(2010) Dandan Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Computational approaches for understanding the evolution of DNA methylation in animals

(2010) Soojin V. Yi et al.   Epigenetics

DNA Methylation and Genome Evolution in Honeybee: Gene Length, Expression, Functional Enrichment Covary with the Evolutionary Signature of DNA Methylation

(2010) Jia Zeng et al.   Genome Biology and Evolution

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

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

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

CpG islands - ‘A rough guide’

(2009) Robert S. Illingworth et al.   FEBS LETTERS

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

(2009) N. Elango et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

DNA Methylation and Structural and Functional Bimodality of Vertebrate Promoters

(2008) N. Elango et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

(2008) Robert Illingworth et al.   PLOS BIOLOGY

Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation

(2008) Navin Elango et al.   PLoS Computational Biology