Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

A Two-Step Process for Epigenetic Inheritance in Arabidopsis

(2014) Todd Blevins et al.   MOLECULAR CELL

SHOOT GROWTH1 Maintains Arabidopsis Epigenomes by Regulating IBM1

(2014) Vincent Coustham et al.   PLoS One

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

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

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

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

Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat

(2013) Abdul Khan et al.   BMC PLANT BIOLOGY

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

Epigenetics and plant genome evolution

(2013) Concepcion M Diez et al.   CURRENT OPINION IN PLANT BIOLOGY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

Genome-Wide Survey and Comparative Analysis of LTR Retrotransposons and Their Captured Genes in Rice and Sorghum

(2013) Shu-Ye Jiang et al.   PLoS One

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

Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns

(2013) M. Lei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication

(2013) T. Tsuchiya 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

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

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

(2012) Jiamu Du et al.   CELL

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

(2012) Mélanie Rigal et al.   EMBO JOURNAL

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus

(2012) Michael Cowley et al.   NUCLEIC ACIDS RESEARCH

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

Birth, death and subfunctionalization in the Arabidopsis genome

(2012) Matthew T. Rutter et al.   TRENDS IN PLANT SCIENCE

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Expanded functions for a family of plant intracellular immune receptors beyond specific recognition of pathogen effectors

(2011) V. Bonardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome

(2010) Soichi Inagaki et al.   EMBO JOURNAL

Lowly Expressed Genes in Arabidopsis thaliana Bear the Signature of Possible Pseudogenization by Promoter Degradation

(2010) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) Asuka Miura et al.   EMBO JOURNAL

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

(2009) Steven Lockton et al.   JOURNAL OF MOLECULAR EVOLUTION

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

(2009) Piotr A. Ziolkowski et al.   NUCLEIC ACIDS RESEARCH

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

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

(2008) Ryan Lister et al.   CELL

Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading

(2008) I. R. Henderson et al.   GENES & DEVELOPMENT

Regulation of alternative polyadenylation by genomic imprinting

(2008) A. J. Wood et al.   GENES & DEVELOPMENT

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

(2008) Nicolas Buisine et al.   GENOMICS

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Control of Genic DNA Methylation by a jmjC Domain-Containing Protein in Arabidopsis thaliana

(2008) H. Saze et al.   SCIENCE