Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa

(2020) Miriam Payá-Milans et al.   GigaScience

Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice

(2019) Alexandre P. Marand et al.   PLANT CELL

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

(2019) Fei He et al.   NATURE GENETICS

Chromatin Remodeling and Epigenetic Regulation in Plant DNA Damage Repair

(2019) Jin-Hong Kim   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells

(2018) Gundula Streubel et al.   MOLECULAR CELL

Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

(2018) Sarah Marburger et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Telomere repeats induce domains of H3K27 methylation in Neurospora

(2018) Kirsty Jamieson et al.   eLife

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

(2018) Hong-Qing Ling et al.   NATURE

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

(2018) Silong Sun et al.   NATURE GENETICS

Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory

(2018) Qing Huan et al.   NEW PHYTOLOGIST

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

The transcriptional landscape of polyploid wheat

(2018) R. H. Ramírez-González et al.   SCIENCE

Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B

(2018) Jan Dvorak et al.   THEORETICAL AND APPLIED GENETICS

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

(2018) Cuijun Zhang et al.   Nature Communications

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

(2017) Benoit Darrier et al.   GENETICS

Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes

(2017) Pei Du et al.   GENOME

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize

(2017) Yan He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

(2017) Benoit Darrier et al.   GENETICS

Silencing of Transposable Elements by piRNAs in Drosophila : An Evolutionary Perspective

(2017) Shiqi Luo et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton

(2016) Dewei Zheng et al.   PLANT PHYSIOLOGY

Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids

(2016) Dae Kwan Ko et al.   PLoS Genetics

The wondrous cycles of polyploidy in plants

(2015) Jonathan F. Wendel   AMERICAN JOURNAL OF BOTANY

Epigenetic and developmental regulation in plant polyploids

(2015) Qingxin Song 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

Dimethylated H3K27 Is a Repressive Epigenetic Histone Mark in the ProtistEntamoeba histolyticaand Is Significantly Enriched in Genes Silenced via the RNAi Pathway

(2015) Bardees M. Foda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis

(2015) Shay Shilo et al.   PLANT CELL

The polyploidy revolution then...and now: Stebbins revisited

(2014) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Redundant Mechanisms to Form Silent Chromatin at Pericentromeric Regions Rely on BEND3 and DNA Methylation

(2014) Nehmé Saksouk et al.   MOLECULAR CELL

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

(2014) Jonathan I. Gent et al.   PLANT CELL

Asymmetric Epigenetic Modification and Elimination of rDNA Sequences by Polyploidization in Wheat

(2014) Xiang Guo et al.   PLANT CELL

Evolution of the BBAA Component of Bread Wheat during Its History at the Allohexaploid Level

(2014) Huakun Zhang et al.   PLANT CELL

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

(2013) P. P. Shah et al.   GENES & DEVELOPMENT

A Fast Estimate for the Population Recombination Rate Based on Regression

(2013) K. Lin et al.   GENETICS

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes

(2013) Jin He et al.   NATURE CELL BIOLOGY

De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment

(2013) Ivan Olovnikov et al.   NUCLEIC ACIDS RESEARCH

Copy number variation of transposable elements in Triticum–Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization

(2013) Beery Yaakov et al.   PLANT CELL REPORTS

Characterization of the LTR retrotransposon repertoire of a plant clade of six diploid and one tetraploid species

(2013) Mathieu Piednoël et al.   PLANT JOURNAL

Sequence-Based Analysis of Translocations and Inversions in Bread Wheat (Triticum aestivum L.)

(2013) Jian Ma et al.   PLoS One

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Genomic and Gene-Level Distribution of Histone H3 Dimethyl Lysine-27 (H3K27me2) in Arabidopsis

(2012) Sunchung Park et al.   PLoS One

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

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

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

Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis

(2012) Lidija Berke et al.   GENOME BIOLOGY

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Histone Methylation in Higher Plants

(2010) Chunyan Liu et al.   Annual Review of Plant Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genetic and Epigenetic Dynamics of a Retrotransposon After Allopolyploidization of Wheat

(2010) Z. Kraitshtein et al.   GENETICS

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

(2010) F. Baudat et al.   SCIENCE

Molecular mechanisms of polyploidy and hybrid vigor

(2010) Z. Jeffrey Chen   TRENDS IN PLANT SCIENCE

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Reactivation of an Inactive Centromere Reveals Epigenetic and Structural Components for Centromere Specification in Maize

(2009) F. Han et al.   PLANT CELL

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Clues to the Evolutionary Success of Polyploid Plants

(2008) Matthew J. Hegarty et al.   CURRENT BIOLOGY

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

(2008) Yana V. Bernatavichute et al.   PLoS One

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE

Managing meiotic recombination in plant breeding

(2008) E WIJNKER et al.   TRENDS IN PLANT SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY