The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

Differences in Effective Ploidy Drive Genome-Wide Endosperm Expression Polarization and Seed Failure in Wild Tomato Hybrids

(2019) Morgane Roth et al.   GENETICS

Auxin regulates endosperm cellularization in Arabidopsis

(2019) Rita A. Batista et al.   GENES & DEVELOPMENT

Paternally acting canonical RNA-directed DNA methylation pathway genes sensitize Arabidopsis endosperm to paternal genome dosage

(2019) P.R. V. Satyaki et al.   PLANT CELL

Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

(2018) Niels Aerts et al.   BMC PLANT BIOLOGY

Paternal easiRNAs regulate parental genome dosage in Arabidopsis

(2018) German Martinez et al.   NATURE GENETICS

Telobox motifs recruit CLF/SWN–PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis

(2018) Yue Zhou et al.   NATURE GENETICS

Sequestration of a Transposon-Derived siRNA by a Target Mimic Imprinted Gene Induces Postzygotic Reproductive Isolation in Arabidopsis

(2018) Guifeng Wang et al.   DEVELOPMENTAL CELL

Anthropoid primate–specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length

(2018) Caitlin E. Dunn-Fletcher et al.   PLOS BIOLOGY

Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana

(2018) Dijun Chen et al.   Nature Communications

A variably imprinted epiallele impacts seed development

(2018) Daniela Pignatta et al.   PLoS Genetics

Endosperm-specific transcriptome analysis by applying the INTACT system

(2018) Gerardo Del Toro-De León et al.   Plant Reproduction

Ectopic application of the repressive histone modification H3K9me2 establishes post-zygotic reproductive isolation in Arabidopsis thaliana

(2017) Hua Jiang et al.   GENES & DEVELOPMENT

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

(2017) Jun Xiao et al.   NATURE GENETICS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles

(2017) Jordi Moreno-Romero et al.   Nature Protocols

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

(2017) Michiel Van Bel et al.   NUCLEIC ACIDS RESEARCH

Widespread Contamination of Arabidopsis Embryo and Endosperm Transcriptome Data Sets

(2017) Michael A. Schon et al.   PLANT CELL

Differences in DNA Binding Specificity of Floral Homeotic Protein Complexes Predict Organ-Specific Target Genes

(2017) Cezary Smaczniak et al.   PLANT CELL

Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA

(2017) Friederike Laprell et al.   SCIENCE

Causal role for inheritance of H3K27me3 in maintaining the OFF state of a Drosophila HOX gene

(2017) Rory T. Coleman et al.   SCIENCE

A Small RNA Pathway Mediates Allelic Dosage in Endosperm

(2017) Robert M. Erdmann et al.   Cell Reports

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

Parental epigenetic asymmetry of PRC2‐mediated histone modifications in theArabidopsisendosperm

(2016) Jordi Moreno‐Romero et al.   EMBO JOURNAL

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae

(2016) Marcelinus R. Hatorangan et al.   PLANT CELL

Auxin production in the endosperm drives seed coat development in Arabidopsis

(2016) Duarte D Figueiredo et al.   eLife

Positional distribution of transcription factor binding sites in Arabidopsis thaliana

(2016) Chun-Ping Yu et al.   Scientific Reports

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

(2015) Bernat Gel et al.   BIOINFORMATICS

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

(2015) Jose M. Muiño et al.   MOLECULAR BIOLOGY AND EVOLUTION

Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources

(2015) Xiaobo Wang et al.   Database-The Journal of Biological Databases and Curation

Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm

(2015) Carolin A. Rebernig et al.   PLoS Genetics

Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

(2015) Philip Wolff et al.   eLife

Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation

(2015) Zhi-Ping Wang et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Auxin production couples endosperm development to fertilization

(2015) Duarte D. Figueiredo et al.   Nature Plants

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hypomethylated Pollen Bypasses the Interploidy Hybridization Barrier in Arabidopsis

(2014) N. Schatlowski et al.   PLANT CELL

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution ofBrassicaspecies

(2014) Elizabeth Hénaff et al.   PLANT JOURNAL

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

(2014) Daniela Pignatta et al.   eLife

Genomic Imprinting: Insights From Plants

(2013) Mary Gehring   Annual Review of Genetics

Embryo and endosperm, partners in seed development

(2013) Clément Lafon-Placette et al.   CURRENT OPINION IN PLANT BIOLOGY

ZHOUPI controls embryonic cuticle formation via a signalling pathway involving the subtilisin protease ABNORMAL LEAF-SHAPE1 and the receptor kinases GASSHO1 and GASSHO2

(2013) Q. Xing et al.   DEVELOPMENT

An Imprinted Gene Underlies Postzygotic Reproductive Isolation in Arabidopsis thaliana

(2013) David Kradolfer et al.   DEVELOPMENTAL CELL

Endogenous retroviruses function as species-specific enhancer elements in the placenta

(2013) Edward B Chuong et al.   NATURE GENETICS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Dissection of two major components of the post-zygotic hybridization barrier in rice endosperm

(2013) Daisuke Sekine et al.   PLANT JOURNAL

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

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

Endosperm cellularization defines an important developmental transition for embryo development

(2012) E. Hehenberger et al.   DEVELOPMENT

Tearing down barriers: understanding the molecular mechanisms of interploidy hybridizations

(2012) N. Schatlowski et al.   JOURNAL OF EXPERIMENTAL BOTANY

Parental genome imbalance in Brassica oleracea causes asymmetric triploid block

(2012) Andrew I. Stoute et al.   PLANT JOURNAL

Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds

(2012) J. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Auxin Biosynthesis: A Simple Two-Step Pathway Converts Tryptophan to Indole-3-Acetic Acid in Plants

(2011) Yunde Zhao   Molecular Plant

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis ULTRAVIOLET-B-INSENSITIVE4 Maintains Cell Division Activity by Temporal Inhibition of the Anaphase-Promoting Complex/Cyclosome

(2011) J. Heyman et al.   PLANT CELL

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

(2011) Mary Gehring et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Polycomb group proteins are required to couple seed coat initiation to fertilization

(2011) P. Roszak 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

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

(2011) Philip Wolff et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana

(2010) Sushma Tiwari et al.   BMC PLANT BIOLOGY

ENDOSPERM FORMATION AFTER 2x, 4x CROSSES IN CERTAIN CEREALS, ESPECIALLY IN HORDEUM VULGARE

(2010) ARTUR HÅKANSSON   HEREDITAS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Rice interspecies hybrids show precocious or delayed developmental transitions in the endosperm without change to the rate of syncytial nuclear division

(2010) Ryo Ishikawa et al.   PLANT JOURNAL

An Atlas of Type I MADS Box Gene Expression during Female Gametophyte and Seed Development in Arabidopsis

(2010) Marian Bemer et al.   PLANT PHYSIOLOGY

The impact of the triploid block on the origin and evolution of polyploid plants

(2010) Claudia Köhler et al.   TRENDS IN GENETICS

H3K27me3 Profiling of the Endosperm Implies Exclusion of Polycomb Group Protein Targeting by DNA Methylation

(2010) Isabelle Weinhofer et al.   PLoS Genetics

Parental Genome Dosage Imbalance Deregulates Imprinting in Arabidopsis

(2010) Pauline E. Jullien et al.   PLoS Genetics

A hitchhiker's guide to the MADS world of plants

(2010) Lydia Gramzow et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Dosage-Dependent Deregulation of an AGAMOUS-LIKE Gene Cluster Contributes to Interspecific Incompatibility

(2009) Harkamal Walia et al.   CURRENT BIOLOGY

Control of PHERES1 Imprinting in Arabidopsis by Direct Tandem Repeats

(2009) Corina Belle R. Villar et al.   Molecular Plant

Turning Meiosis into Mitosis

(2009) Isabelle d'Erfurth et al.   PLOS BIOLOGY

Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis

(2009) Aleksandra Erilova et al.   PLoS Genetics

The endosperm-specific ZHOUPI gene of Arabidopsis thaliana regulates endosperm breakdown and embryonic epidermal development

(2008) S. Yang et al.   DEVELOPMENT

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

The AGL62 MADS Domain Protein Regulates Cellularization during Endosperm Development in Arabidopsis

(2008) I.-H. Kang et al.   PLANT CELL

The Transport of Sugars to Developing Embryos Is Not via the Bulk Endosperm in Oilseed Rape Seeds

(2008) E. R. Morley-Smith et al.   PLANT PHYSIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY