Integrative epigenomic mapping defines four main chromatin states in Arabidopsis.

PubWeight™: 3.16‹?› | Rank: Top 1%

🔗 View Article (PMC 3098477)

Published in EMBO J on April 12, 2011

Authors

François Roudier1, Ikhlak Ahmed, Caroline Bérard, Alexis Sarazin, Tristan Mary-Huard, Sandra Cortijo, Daniel Bouyer, Erwann Caillieux, Evelyne Duvernois-Berthet, Liza Al-Shikhley, Laurène Giraut, Barbara Després, Stéphanie Drevensek, Frédy Barneche, Sandra Dèrozier, Véronique Brunaud, Sébastien Aubourg, Arp Schnittger, Chris Bowler, Marie-Laure Martin-Magniette, Stéphane Robin, Michel Caboche, Vincent Colot

Author Affiliations

1: Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Paris, France. roudier@biologie.ens.fr

Articles citing this

(truncated to the top 100)

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell (2013) 3.27

Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell (2013) 3.02

Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol Cell (2012) 2.85

Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol (2013) 2.71

Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell (2012) 2.19

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol (2013) 2.14

Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science (2012) 1.80

Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr Opin Genet Dev (2012) 1.71

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res (2013) 1.71

Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements. PLoS Genet (2016) 1.50

Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS Genet (2011) 1.48

Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome. Cell Rep (2016) 1.45

Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genet (2012) 1.43

Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell (2012) 1.38

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol (2013) 1.30

Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell (2012) 1.29

Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol (2011) 1.28

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2012) 1.27

Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res (2012) 1.25

Chromatin: constructing the big picture. EMBO J (2011) 1.24

Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol Evol (2013) 1.21

Loss of DNA methylation affects the recombination landscape in Arabidopsis. Proc Natl Acad Sci U S A (2012) 1.20

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States. Plant Cell (2014) 1.16

Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation. Plant Cell (2014) 1.16

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biol (2013) 1.15

Antagonistic roles for H3K36me3 and H3K27me3 in the cold-induced epigenetic switch at Arabidopsis FLC. Curr Biol (2014) 1.12

Epigenetic remodeling of meiotic crossover frequency in Arabidopsis thaliana DNA methyltransferase mutants. PLoS Genet (2012) 1.11

Dynamic deposition of histone variant H3.3 accompanies developmental remodeling of the Arabidopsis transcriptome. PLoS Genet (2012) 1.11

The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet (2013) 1.11

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription. Genes Dev (2014) 1.10

Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. PLoS Genet (2012) 1.10

Polycomb group complexes mediate developmental transitions in plants. Plant Physiol (2011) 1.10

Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Natl Acad Sci U S A (2012) 1.10

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants. Nat Commun (2013) 1.09

Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A (2013) 1.09

The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes Dev (2013) 1.09

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Res (2014) 1.07

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains. Nucleic Acids Res (2014) 1.07

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res (2014) 1.06

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nat Commun (2012) 1.03

H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res (2012) 1.02

CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome. Proc Natl Acad Sci U S A (2012) 1.02

Human genome replication proceeds through four chromatin states. PLoS Comput Biol (2013) 1.01

Control of transposon activity by a histone H3K4 demethylase in rice. Proc Natl Acad Sci U S A (2013) 1.00

Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell (2011) 0.99

A chromatin link to caste identity in the carpenter ant Camponotus floridanus. Genome Res (2012) 0.99

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res (2013) 0.99

Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell (2013) 0.98

Epigenetic regulation in plants. Cold Spring Harb Perspect Biol (2014) 0.98

The First Rule of Plant Transposable Element Silencing: Location, Location, Location. Plant Cell (2016) 0.96

Interplay between active chromatin marks and RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet (2013) 0.94

Jumonji C domain protein JMJ705-mediated removal of histone H3 lysine 27 trimethylation is involved in defense-related gene activation in rice. Plant Cell (2013) 0.94

Ordered changes in histone modifications at the core of the Arabidopsis circadian clock. Proc Natl Acad Sci U S A (2012) 0.93

Dynamic epigenetic regulation of gene expression during the life cycle of malaria parasite Plasmodium falciparum. PLoS Pathog (2013) 0.93

Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis. PLoS Genet (2012) 0.90

The dynamics of histone H3 modifications is species-specific in plant meiosis. Planta (2013) 0.89

Evolutionarily conserved histone methylation dynamics during seed life-cycle transitions. PLoS One (2012) 0.89

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin. Genome Res (2015) 0.89

Different gene-specific mechanisms determine the 'revised-response' memory transcription patterns of a subset of A. thaliana dehydration stress responding genes. Nucleic Acids Res (2014) 0.88

Analysis of the epigenetic status of telomeres by using ChIP-seq data. Nucleic Acids Res (2012) 0.88

Mechanisms guiding Polycomb activities during gene silencing in Arabidopsis thaliana. Front Plant Sci (2013) 0.88

The stem cell state in plant development and in response to stress. Front Plant Sci (2011) 0.88

Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm. EMBO J (2016) 0.87

Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements. Genome Biol (2012) 0.87

Mutations in EDM2 selectively affect silencing states of transposons and induce plant developmental plasticity. Sci Rep (2013) 0.87

The Arabidopsis GAGA-Binding Factor BASIC PENTACYSTEINE6 Recruits the POLYCOMB-REPRESSIVE COMPLEX1 Component LIKE HETEROCHROMATIN PROTEIN1 to GAGA DNA Motifs. Plant Physiol (2015) 0.86

A novel HSI2 mutation in Arabidopsis affects the PHD-like domain and leads to derepression of seed-specific gene expression. Planta (2012) 0.86

Chromatin-dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins. Plant Cell (2014) 0.86

Arabidopsis MRG domain proteins bridge two histone modifications to elevate expression of flowering genes. Nucleic Acids Res (2014) 0.86

Dynamics of H3K27me3 methylation and demethylation in plant development. Plant Signal Behav (2015) 0.86

Ectopic gene expression and organogenesis in Arabidopsis mutants missing BRU1 required for genome maintenance. Genetics (2011) 0.85

Histone monoubiquitylation position determines specificity and direction of enzymatic cross-talk with histone methyltransferases Dot1L and PRC2. J Biol Chem (2012) 0.85

Making sense of chromatin states. Nat Methods (2011) 0.85

chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. Nucleic Acids Res (2013) 0.84

DNA DAMAGE BINDING PROTEIN 2 (DDB2) Shapes the DNA Methylation Landscape. Plant Cell (2016) 0.84

Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei. Plant Mol Biol (2015) 0.84

Seed dormancy cycling in Arabidopsis: chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals. Plant J (2014) 0.83

A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence. Plant Physiol (2015) 0.83

Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster. Chromosoma (2013) 0.83

Protocol: Chromatin immunoprecipitation (ChIP) methodology to investigate histone modifications in two model diatom species. Plant Methods (2012) 0.82

Long non-coding RNAs and their biological roles in plants. Genomics Proteomics Bioinformatics (2015) 0.82

Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes. Plant Physiol (2015) 0.82

Genetic sources of population epigenomic variation. Nat Rev Genet (2016) 0.82

The Armadillo repeat gene ZAK IXIK promotes Arabidopsis early embryo and endosperm development through a distinctive gametophytic maternal effect. Plant Cell (2012) 0.81

Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator. Nucleic Acids Res (2013) 0.81

HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing. Plant Physiol (2015) 0.81

eQTL mapping of transposon silencing reveals a position-dependent stable escape from epigenetic silencing and transposition of AtMu1 in the Arabidopsis lineage. Plant Cell (2014) 0.81

Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14. Nucleic Acids Res (2015) 0.81

The phenotypic predisposition of the parent in F1 hybrid is correlated with transcriptome preference of the positive general combining ability parent. BMC Genomics (2014) 0.81

Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis. Plant Cell (2013) 0.81

Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters. Plant Physiol (2015) 0.81

Developmental silencing of the AtTERT gene is associated with increased H3K27me3 loading and maintenance of its euchromatic environment. J Exp Bot (2012) 0.80

Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency. PLoS Comput Biol (2015) 0.80

The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell (2015) 0.80

Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana. Front Plant Sci (2015) 0.80

Chromatin dynamics during plant sexual reproduction. Front Plant Sci (2014) 0.80

Chromatin dynamics during cellular differentiation in the female reproductive lineage of flowering plants. Plant J (2015) 0.80

Perspectives: using polymer modeling to understand the formation and function of nuclear compartments. Chromosome Res (2017) 0.79

Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration. Mob DNA (2013) 0.79

Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster. BMC Plant Biol (2013) 0.79

Articles cited by this

Translating the histone code. Science (2001) 56.77

Chromatin modifications and their function. Cell (2007) 55.98

The language of covalent histone modifications. Nature (2000) 44.92

Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78

Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28

A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39

The complex language of chromatin regulation during transcription. Nature (2007) 16.97

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell (2006) 15.24

Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics (2009) 12.01

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet (2006) 11.88

Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51

Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol (2010) 9.84

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78

Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell (2010) 9.50

Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11

Regulation of alternative splicing by histone modifications. Science (2010) 7.98

Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet (2010) 7.39

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature (2010) 6.87

Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res (2006) 6.75

Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol (2005) 6.37

Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol Cell (2005) 5.96

Relationship between nucleosome positioning and DNA methylation. Nature (2010) 5.27

Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol (2006) 5.01

Histone ubiquitination: triggering gene activity. Mol Cell (2008) 4.42

Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol (2007) 4.30

Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol (2007) 4.29

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature (2008) 4.20

Genome-wide views of chromatin structure. Annu Rev Biochem (2009) 3.89

Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol (2009) 3.61

The language of histone crosstalk. Cell (2010) 3.18

Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet (2007) 3.11

Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells. Nat Cell Biol (2008) 3.08

Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma (2004) 3.00

Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation. Mol Cell (2009) 2.91

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol (2009) 2.86

Crosstalk among Histone Modifications. Cell (2008) 2.70

Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One (2008) 2.69

Is there a code embedded in proteins that is based on post-translational modifications? Nat Rev Mol Cell Biol (2008) 2.64

Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation. Proc Natl Acad Sci U S A (2008) 2.44

Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res (2010) 2.36

Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res (2004) 2.28

Characterization of human epigenomes. Curr Opin Genet Dev (2009) 2.17

Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods (2005) 2.10

Chromosomal histone modification patterns--from conservation to diversity. Trends Plant Sci (2006) 2.09

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res (2010) 1.87

ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol (2009) 1.85

Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature (2007) 1.81

Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet (2011) 1.79

Repression of FLOWERING LOCUS C and FLOWERING LOCUS T by the Arabidopsis Polycomb repressive complex 2 components. PLoS One (2008) 1.76

CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. Nucleic Acids Res (2007) 1.72

Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol (2008) 1.68

Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet (2008) 1.63

Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature (2010) 1.63

FLAGdb++: a database for the functional analysis of the Arabidopsis genome. Nucleic Acids Res (2004) 1.61

A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Res (2010) 1.58

A chromatin link that couples cell division to root epidermis patterning in Arabidopsis. Nature (2007) 1.56

Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell (2008) 1.54

Epigenetic modifications in plants: an evolutionary perspective. Curr Opin Plant Biol (2011) 1.45

Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell (2009) 1.43

Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. Plant Cell (2010) 1.23

Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends Genet (2009) 1.22

Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genet (2010) 1.16

Repression of the floral transition via histone H2B monoubiquitination. Plant J (2008) 1.15

Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis. Plant Physiol (2008) 1.08

ChIPmix: mixture model of regressions for two-color ChIP-chip analysis. Bioinformatics (2008) 1.05

Regulation of cell identity by plant Polycomb and trithorax group proteins. Curr Opin Genet Dev (2010) 0.99

ANCORP: a high-resolution approach that generates distinct chromatin state models from multiple genome-wide datasets. Plant J (2010) 0.89

Articles by these authors

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04

Ensembl 2013. Nucleic Acids Res (2012) 11.70

The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15

Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (2004) 9.97

Mapping human genetic diversity in Asia. Science (2009) 7.40

Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell (2004) 7.11

Understanding mechanisms of novel gene expression in polyploids. Trends Genet (2003) 4.90

Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet (2009) 4.57

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc Natl Acad Sci U S A (2006) 4.52

Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev (2005) 4.50

Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science (2002) 4.49

A role for RNAi in the selective correction of DNA methylation defects. Science (2009) 4.30

Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol (2007) 4.29

The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature (2010) 3.60

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58

Genetics and biochemistry of seed flavonoids. Annu Rev Plant Biol (2006) 3.55

TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J (2004) 3.45

Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science (2009) 3.31

Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods (2005) 3.28

Mapping the epigenetic basis of complex traits. Science (2014) 3.13

Epigenome dynamics: a quantitative genetics perspective. Nat Rev Genet (2008) 3.13

Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet (2007) 3.11

State transitions and light adaptation require chloroplast thylakoid protein kinase STN7. Nature (2005) 3.07

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02

Retracted RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet (2013) 2.91

A holistic approach to marine eco-systems biology. PLoS Biol (2011) 2.71

Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat Biotechnol (2005) 2.41

Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell (2005) 2.40

A stress surveillance system based on calcium and nitric oxide in marine diatoms. PLoS Biol (2006) 2.40

CATMA: a complete Arabidopsis GST database. Nucleic Acids Res (2003) 2.34

Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc Natl Acad Sci U S A (2008) 2.26

Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development. Plant Cell (2003) 2.18

A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS One (2008) 2.17

The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell (2008) 2.15

Concern Misregulation of AUXIN RESPONSE FACTOR 8 underlies the developmental abnormalities caused by three distinct viral silencing suppressors in Arabidopsis. PLoS Pathog (2011) 2.12

Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods (2005) 2.10

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature (2011) 2.06

Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene (2007) 2.05

Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J (2008) 2.02

Classification and identification of Arabidopsis cell wall mutants using Fourier-Transform InfraRed (FT-IR) microspectroscopy. Plant J (2003) 1.98

Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation. PLoS Genet (2009) 1.96

Bypassing genomic imprinting allows seed development. Nature (2007) 1.91

A positive signal from the fertilization of the egg cell sets off endosperm proliferation in angiosperm embryogenesis. Nat Genet (2005) 1.87

Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family. EMBO Rep (2003) 1.87

Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet (2011) 1.79

TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat. Plant Cell (2005) 1.79

Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis. Plant J (2005) 1.78

Novel functions of plant cyclin-dependent kinase inhibitors, ICK1/KRP1, can act non-cell-autonomously and inhibit entry into mitosis. Plant Cell (2005) 1.72

CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. Nucleic Acids Res (2007) 1.72

Misexpression of the cyclin-dependent kinase inhibitor ICK1/KRP1 in single-celled Arabidopsis trichomes reduces endoreduplication and cell size and induces cell death. Plant Cell (2003) 1.71

Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays. BMC Plant Biol (2010) 1.71

Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc Natl Acad Sci U S A (2004) 1.70

Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots". Genome Res (2005) 1.70

Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res (2009) 1.67

Molecular control and function of endoreplication in development and physiology. Trends Plant Sci (2011) 1.67

TT8 controls its own expression in a feedback regulation involving TTG1 and homologous MYB and bHLH factors, allowing a strong and cell-specific accumulation of flavonoids in Arabidopsis thaliana. Plant J (2006) 1.65

Ectopic D-type cyclin expression induces not only DNA replication but also cell division in Arabidopsis trichomes. Proc Natl Acad Sci U S A (2002) 1.65

Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res (2004) 1.63

VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data. Bioinformatics (2004) 1.63

FLAGdb++: a database for the functional analysis of the Arabidopsis genome. Nucleic Acids Res (2004) 1.61

Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana. Planta (2006) 1.61

The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat. Plant Cell (2002) 1.58

Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. Plant J (2007) 1.58

LEAFY COTYLEDON 2 activation is sufficient to trigger the accumulation of oil and seed specific mRNAs in Arabidopsis leaves. FEBS Lett (2005) 1.57

Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106. Plant Physiol (2008) 1.53

Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Mol Genet Genomics (2007) 1.52

A diatom gene regulating nitric-oxide signaling and susceptibility to diatom-derived aldehydes. Curr Biol (2008) 1.48

Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell (2003) 1.48

The photomorphogenesis regulator DET1 binds the amino-terminal tail of histone H2B in a nucleosome context. Curr Biol (2002) 1.46

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics (2008) 1.45

T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep (2002) 1.44

Multifunctional acetyl-CoA carboxylase 1 is essential for very long chain fatty acid elongation and embryo development in Arabidopsis. Plant J (2003) 1.43

An atypical member of the light-harvesting complex stress-related protein family modulates diatom responses to light. Proc Natl Acad Sci U S A (2010) 1.42

The INO80 protein controls homologous recombination in Arabidopsis thaliana. Mol Cell (2004) 1.41

Endosperm: an integrator of seed growth and development. Curr Opin Plant Biol (2006) 1.40

Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet (2013) 1.40

An eIF4E allele confers resistance to an uncapped and non-polyadenylated RNA virus in melon. Plant J (2006) 1.39

Switching the cell cycle. Kip-related proteins in plant cell cycle control. Plant Physiol (2005) 1.39

Comparative genomics of the pennate diatom Phaeodactylum tricornutum. Plant Physiol (2005) 1.39

Genome properties of the diatom Phaeodactylum tricornutum. Plant Physiol (2002) 1.38

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Res (2011) 1.35