Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

Kin Conflict in Seed Development: An Interdependent but Fractious Collective

(2013) David Haig   Annual Review of Cell and Developmental Biology

Genomic Imprinting: Insights From Plants

(2013) Mary Gehring   Annual Review of Genetics

RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis

(2013) T. M. Vu et al.   DEVELOPMENT

An Imprinted Gene Underlies Postzygotic Reproductive Isolation in Arabidopsis thaliana

(2013) David Kradolfer et al.   DEVELOPMENTAL CELL

Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize

(2013) M. Zhang et al.   GENOME RESEARCH

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm Development

(2013) M. Xin et al.   PLANT CELL

Paternally expressed genes predominate in the placenta

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

Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm

(2013) J. A. Rodrigues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed

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

Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species

(2013) A. J. Waters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

Epigenetic Mechanisms Underlying Genomic Imprinting in Plants

(2012) Claudia Köhler et al.   Annual Review of Plant Biology

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

DNA Methylation Dynamics during Sexual Reproduction in Arabidopsis thaliana

(2012) Pauline E. Jullien et al.   CURRENT BIOLOGY

Evolution, function, and regulation of genomic imprinting in plant seed development

(2012) H. Jiang et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2012) C. A. Ibarra et al.   SCIENCE

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective

(2012) Brian DeVeale et al.   PLoS Genetics

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm

(2011) A. J. Waters et al.   PLANT CELL

Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds

(2011) Mary Gehring et al.   PLoS One

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte

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

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

(2011) M. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of imprinted gene expression inArabidopsisendosperm

(2011) Tzung-Fu Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation

(2011) Marcel Lafos et al.   PLoS Genetics

A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

(2011) Ming Luo et al.   PLoS Genetics

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm

(2011) Philip Wolff et al.   PLoS Genetics

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

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

Genetic analysis of two OsLpa1-like genes in Arabidopsis reveals that only one is required for wild-type seed phytic acid levels

(2010) Sang-Ic Kim et al.   PLANTA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin

(2009) Vera K Schoft et al.   EMBO REPORTS

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

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

(2009) Rebecca A. Mosher et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

PHYTOCHROME B and HISTONE DEACETYLASE 6 Control Light-Induced Chromatin Compaction in Arabidopsis thaliana

(2009) Federico Tessadori et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Kismeth: Analyzer of plant methylation states through bisulfite sequencing

(2008) Eyal Gruntman et al.   BMC BIOINFORMATICS

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

(2008) Ryan Lister et al.   CELL

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH