Monitoring the interplay between transposable element families and DNA methylation in maize

Dynamics and function of DNA methylation in plants

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

Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome

(2018) Hainan Zhao et al.   PLANT PHYSIOLOGY

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

The dominant and poor penetrant phenotypes of the maize mutation Unstable factor for orange1 are caused by DNA methylation changes at a linked transposon

(2018) Kameron Wittmeyer et al.   PLANT CELL

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice

(2017) Jae Young Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

Integration of omic networks in a developmental atlas of maize

(2016) J. W. Walley et al.   SCIENCE

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

Epigenetic transitions leading to heritable, RNA-mediated de novo silencing inArabidopsis thaliana

(2015) Donna M. Bond et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Control of transposable elements in Arabidopsis thaliana

(2014) Hidetaka Ito et al.   CHROMOSOME RESEARCH

Genetic Perturbation of the Maize Methylome

(2014) Qing Li et al.   PLANT CELL

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

(2014) S. R. Eichten et al.   PLANT PHYSIOLOGY

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

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

DNA methylation as a system of plant genomic immunity

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

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

(2013) M. Regulski et al.   GENOME RESEARCH

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

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

Mu-seq: Sequence-Based Mapping and Identification of Transposon Induced Mutations

(2013) Donald R. McCarty et al.   PLoS One

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

(2012) Jiamu Du et al.   CELL

Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata

(2012) S. Tsukahara et al.   GENES & DEVELOPMENT

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

(2012) J. I. Gent et al.   GENOME RESEARCH

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

(2012) Steven R. Eichten et al.   PLoS Genetics

Transposable element origins of epigenetic gene regulation

(2011) Damon Lisch et al.   CURRENT OPINION IN PLANT BIOLOGY

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

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

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

Genome-Wide Distribution of TransposedDissociationElements in Maize

(2010) Erik Vollbrecht et al.   PLANT CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

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

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

(2009) Antoine Martin et al.   NATURE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE