Epigenetic regulation and epigenomic landscape in rice

DNA Methylation Affects Gene Alternative Splicing in Plants: An Example from Rice

(2016) Xutong Wang et al.   Molecular Plant

OsVIL1 controls flowering time in rice by suppressing OsLF under short days and by inducing Ghd7 under long days

(2016) Hee Joong Jeong et al.   PLANT CELL REPORTS

A Signaling Cascade from miR444 to RDR1 in Rice Antiviral RNA Silencing Pathway

(2016) Huacai Wang et al.   PLANT PHYSIOLOGY

Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways

(2016) Feng Tan et al.   PLANT PHYSIOLOGY

The effect of transposable elements on phenotypic variation: insights from plants to humans

(2016) Liya Wei et al.   Science China-Life Sciences

Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine

(2016) Yi Chen Lu et al.   Scientific Reports

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

(2015) Wensheng Wang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Global epigenomic analysis indicates that Epialleles contribute to Allele-specific expression via Allele-specific histone modifications in hybrid rice

(2015) Zhibin Guo et al.   BMC GENOMICS

Genome-wide analysis of DNA methylation in photoperiod- and thermo-sensitive male sterile rice Peiai 64S

(2015) Jihong Hu et al.   BMC GENOMICS

Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation

(2015) Yong Zhang et al.   CELL RESEARCH

A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice

(2015) Jiang Hu et al.   Molecular Plant

Gene Body CG and CHG Methylation and Suppression of Centromeric CHH Methylation are Mediated by DECREASE IN DNA METHYLATION1 in Rice

(2015) Hisataka Numa et al.   Molecular Plant

The karma of oil palms

(2015) Jerzy Paszkowski   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

Rice microRNA osa-miR1848 targets the obtusifoliol 14α-demethylase geneOsCYP51G3and mediates the biosynthesis of phytosterols and brassinosteroids during development and in response to stress

(2015) Kuaifei Xia et al.   NEW PHYTOLOGIST

Regulation of Histone Methylation and Reprogramming of Gene Expression in the Rice Inflorescence Meristem

(2015) Xiaoyun Liu et al.   PLANT CELL

Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition

(2015) Chaoyang Cheng et al.   PLANT JOURNAL

Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits

(2015) Huan Wang et al.   PLANT JOURNAL

Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice

(2015) Song Xianwei et al.   PLANT PHYSIOLOGY

MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice

(2015) Jing Jin et al.   PLANT PHYSIOLOGY

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development

(2015) Mei-Qing Xing et al.   PLANT PHYSIOLOGY

Coordinated regulation of vegetative and reproductive branching in rice

(2015) Lei Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

(2015) Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coding function for non-coding RNA in plants—insights from miRNA encoded peptide (miPEP)

(2015) Long Wang et al.   Science China-Life Sciences

Transposable elements play an important role during cotton genome evolution and fiber cell development

(2015) Kun Wang et al.   Science China-Life Sciences

Small RNAs in pollen

(2015) Hui He et al.   Science China-Life Sciences

A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

(2015) Hude Mao et al.   Nature Communications

Histone H3K4me3 and H3K27me3 regulatory genes control stable transmission of an epimutation in rice

(2015) Xiangsong Chen et al.   Scientific Reports

Automatic discovery of cell types and microcircuitry from neural connectomics

(2015) Eric Jonas et al.   eLife

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

(2015) David Secco et al.   eLife

Viral-inducible Argonaute18 confers broad-spectrum virus resistance in rice by sequestering a host microRNA

(2015) Jianguo Wu et al.   eLife

Profiling the expression domains of a rice-specific microRNA under stress

(2015) Neha Sharma et al.   Frontiers in Plant Science

Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice

(2015) Penggen Duan et al.   Nature Plants

Control of grain size and rice yield by GL2-mediated brassinosteroid responses

(2015) Ronghui Che et al.   Nature Plants

Single cell sequencing: technique, application, and future development

(2015) Ruidong Xue et al.   Science Bulletin

Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress

(2015) Liliana J. Ferreira et al.   PLoS One

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

(2015) Rohini Garg et al.   Scientific Reports

Epigenetic regulation and functional exaptation of transposable elements in higher plants

(2014) Xiekui Cui et al.   CURRENT OPINION IN PLANT BIOLOGY

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

The polycomb group geneEMF2Bis essential for maintenance of floral meristem determinacy in rice

(2014) Liza J. Conrad et al.   PLANT JOURNAL

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs

(2014) Reina Komiya et al.   PLANT JOURNAL

The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice

(2014) Takaki Yamauchi et al.   PLANT MOLECULAR BIOLOGY

Rice Fertilization-Independent Endosperm1 Regulates Seed Size under Heat Stress by Controlling Early Endosperm Development

(2014) J. J. Folsom et al.   PLANT PHYSIOLOGY

Trithorax Group Protein Oryza sativa Trithorax1 Controls Flowering Time in Rice via Interaction with Early heading date3

(2014) S. C. Choi et al.   PLANT PHYSIOLOGY

OsmiR396d-Regulated OsGRFs Function in Floral Organogenesis in Rice through Binding to Their Targets OsJMJ706 and OsCR4

(2014) H. Liu et al.   PLANT PHYSIOLOGY

Divergence of Gene Body DNA Methylation and Evolution of Plant Duplicate Genes

(2014) Jun Wang et al.   PLoS One

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

(2014) L. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality

(2014) L. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice

(2014) Xian Jun Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetics reloaded: the single-cell revolution

(2014) Poonam Bheda et al.   TRENDS IN CELL BIOLOGY

RNase ZS1 processes Ub L40 mRNAs and controls thermosensitive genic male sterility in rice

(2014) Hai Zhou et al.   Nature Communications

The rice enhancer of zeste [E(z)] genes SDG711 and SDG718 are respectively involved in long day and short day signaling to mediate the accurate photoperiod control of flowering time

(2014) Xiaoyun Liu et al.   Frontiers in Plant Science

The 3,000 rice genomes project: new opportunities and challenges for future rice research

(2014) Jia-Yang Li et al.   GigaScience

The 3,000 rice genomes project

(2014)   GigaScience

Non-coding RNAs and DNA methylation in plants

(2014) Yuanyuan Zhao et al.   National Science Review

Functional characterization of a rice de novo DNA methyltransferase, OsDRM2, expressed in Escherichia coli and yeast

(2013) Jinsong Pang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Expression analysis of histone acetyltransferases in rice under drought stress

(2013) Hui Fang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes

(2013) Yujun Han et al.   BMC GENOMICS

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Biogenesis and function of rice small RNAs from non-coding RNA precursors

(2013) Siwaret Arikit et al.   CURRENT OPINION IN PLANT BIOLOGY

Rice epigenomics and epigenetics: challenges and opportunities

(2013) Xiangsong Chen et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

(2013) Zhou Du et al.   Molecular Plant

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching

(2013) Yu-Chan Zhang et al.   NATURE BIOTECHNOLOGY

CRISPRs and epigenome editing

(2013) Nicole Rusk   NATURE METHODS

Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of theNramp6(Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance

(2013) Sonia Campo et al.   NEW PHYTOLOGIST

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

(2013) M. Jabnoune et al.   PLANT CELL

Jumonji C Domain Protein JMJ705-Mediated Removal of Histone H3 Lysine 27 Trimethylation Is Involved in Defense-Related Gene Activation in Rice

(2013) T. Li et al.   PLANT CELL

Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.)

(2013) CHUNHUA YANG et al.   PLANT CELL AND ENVIRONMENT

Histone deacetylases and their functions in plants

(2013) Xujun Ma et al.   PLANT CELL REPORTS

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

Multiple Rice MicroRNAs Are Involved in Immunity against the Blast Fungus Magnaporthe oryzae

(2013) Y. Li et al.   PLANT PHYSIOLOGY

The Rice NAD+-Dependent Histone Deacetylase OsSRT1 Targets Preferentially to Stress- and Metabolism-Related Genes and Transposable Elements

(2013) Xiaochao Zhong et al.   PLoS One

Control of transposon activity by a histone H3K4 demethylase in rice

(2013) X. Cui 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

CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize

(2013) Q. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Polycomb Group Gene OsFIE2 Regulates Rice (Oryza sativa) Seed Development and Grain Filling via a Mechanism Distinct from Arabidopsis

(2013) Babi Ramesh Reddy Nallamilli et al.   PLoS Genetics

Structural Basis of a Histone H3 Lysine 4 Demethylase Required for Stem Elongation in Rice

(2013) Qingfeng Chen et al.   PLoS Genetics

Plants regenerated from tissue culture contain stable epigenome changes in rice

(2013) Hume Stroud et al.   eLife

Molecular dissection of complex agronomic traits of rice: a team effort by Chinese scientists in recent years

(2013) Jianru Zuo et al.   National Science Review

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

(2012) Xin Li et al.   BMC GENOMICS

Histone acetyltransferases in rice (Oryza sativa L.): phylogenetic analysis, subcellular localization and expression

(2012) Xia Liu et al.   BMC PLANT BIOLOGY

A non-coding RNA locus mediates environment-conditioned male sterility in rice

(2012) Danmeng Zhu et al.   CELL RESEARCH

Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA

(2012) Hai Zhou et al.   CELL RESEARCH

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)

(2012) Hiromi Higo et al.   MOLECULAR GENETICS AND GENOMICS

RNA-Directed DNA Methylation Is Involved in Regulating Photoperiod-Sensitive Male Sterility in Rice

(2012) Jihua Ding et al.   Molecular Plant

H3K36 Methylation Is Involved in Promoting Rice Flowering

(2012) Pengfei Sui et al.   Molecular Plant

Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication

(2012) Yu Wang et al.   NEW PHYTOLOGIST

The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice

(2012) C. Sun et al.   PLANT CELL

Identification and Characterization of an Epi-Allele of FIE1 Reveals a Regulatory Linkage between Two Epigenetic Marks in Rice

(2012) L. Zhang et al.   PLANT CELL

HDT701, a Histone H4 Deacetylase, Negatively Regulates Plant Innate Immunity by Modulating Histone H4 Acetylation of Defense-Related Genes in Rice

(2012) B. Ding et al.   PLANT CELL

Targeted disruption of an orthologue of DOMAINS REARRANGED METHYLASE 2, OsDRM2, impairs the growth of rice plants by abnormal DNA methylation

(2012) Satoru Moritoh et al.   PLANT JOURNAL

OsVIL2 functions with PRC2 to induce flowering by repressingOsLFL1in rice

(2012) Jungil Yang et al.   PLANT JOURNAL

A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny

(2012) Akemi Ono et al.   PLANT JOURNAL

Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress

(2012) Wei Zong et al.   PLANT MOLECULAR BIOLOGY

Gradual Increase of miR156 Regulates Temporal Expression Changes of Numerous Genes during Leaf Development in Rice

(2012) K. Xie et al.   PLANT PHYSIOLOGY

Bioinformatic Analysis of Epigenetic and MicroRNA Mediated Regulation of Drought Responsive Genes in Rice

(2012) Rafi Shaik et al.   PLoS One

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

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

CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome

(2012) Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of Transposon-Derived Small RNAs in the Interplay between Genomes and Parasitic DNA in Rice

(2012) Misuzu Nosaka et al.   PLoS Genetics

Miniature Inverted-Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

(2011) C. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

(2011) Yufeng Wu et al.   PLANT CELL

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

(2011) Xianwei Song et al.   PLANT JOURNAL

LEAF TIP NECROSIS1 Plays a Pivotal Role in the Regulation of Multiple Phosphate Starvation Responses in Rice

(2011) B. Hu et al.   PLANT PHYSIOLOGY

Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data

(2011) Brandon M. Malone et al.   PLoS One

A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

(2011) H. La et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone Methylation in Higher Plants

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

Plant virus-mediated induction of miR168 is associated with repression of ARGONAUTE1 accumulation

(2010) Éva Várallyay et al.   EMBO JOURNAL

Overexpression of Osta-siR2141 caused abnormal polarity establishment and retarded growth in rice

(2010) Jiang Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

SDG714 Regulates Specific Gene Expression and Consequently Affects Plant Growth via H3K9 Dimethylation

(2010) Bo Ding et al.   Journal of Integrative Plant Biology

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

Rice SUVH Histone Methyltransferase Genes Display Specific Functions in Chromatin Modification and Retrotransposon Repression

(2010) Fu-Jun Qin et al.   Molecular Plant

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice

(2010) Yongqing Jiao et al.   NATURE GENETICS

OsSPL14 promotes panicle branching and higher grain productivity in rice

(2010) Kotaro Miura et al.   NATURE GENETICS

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

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

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

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

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

(2010) G. He et al.   PLANT CELL

Distinct Regulation of Adaxial-Abaxial Polarity in Anther Patterning in Rice

(2010) T. Toriba et al.   PLANT CELL

Transcriptome-wide identification of microRNA targets in rice

(2010) Yong-Fang Li et al.   PLANT JOURNAL

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice

(2010) Huihuang Yan et al.   PLANT JOURNAL

Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice

(2010) Yongsheng Yan et al.   PLANT JOURNAL

Local DNA hypomethylation activates genes in rice endosperm

(2010) A. Zemach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

DEP and AFO Regulate Reproductive Habit in Rice

(2010) Kejian Wang et al.   PLoS Genetics

Small RNAs and Their Roles in Plant Development

(2009) Xuemei Chen   Annual Review of Cell and Developmental Biology

Rice histone deacetylase genes display specific expression patterns and developmental functions

(2009) Yongfeng Hu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa)

(2009) Qian-Hao Zhu et al.   BMC PLANT BIOLOGY

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

Adaptive Evolution Involving Gene Duplication and Insertion of a Novel Ty1/copia-Like Retrotransposon in Soybean

(2009) Akira Kanazawa et al.   JOURNAL OF MOLECULAR EVOLUTION

Expression, Imprinting, and Evolution of Rice Homologs of the Polycomb Group Genes

(2009) Ming Luo et al.   Molecular Plant

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

Rice MicroRNA Effector Complexes and Targets

(2009) L. Wu et al.   PLANT CELL

A metastable DWARF1 epigenetic mutant affecting plant stature in rice

(2009) K. Miura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Polymerase IV Functions in Paramutation in Zea mays

(2009) K. F. Erhard et al.   SCIENCE

RNA-Silencing Enzymes Pol IV and Pol V in Maize: More than one Flavor?

(2009) Craig S. Pikaard et al.   PLoS Genetics

Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

(2009) Yi Jia et al.   PLoS Genetics

Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

(2009) Jennifer L. Stonaker et al.   PLoS Genetics

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

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

(2008) Ryan Lister et al.   CELL

A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica

(2008) Nobuhiko Oki et al.   GENES & GENETIC SYSTEMS

Comparative Analysis of JmjC Domain-containing Proteins Reveals the Potential Histone Demethylases inArabidopsisand Rice

(2008) Falong Lu et al.   Journal of Integrative Plant Biology

Alternative splicing of the rice OsMET1 genes encoding maintenance DNA methyltransferase

(2008) Takaki Yamauchi et al.   JOURNAL OF PLANT PHYSIOLOGY

Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4

(2008) Ben-Liang Yin et al.   Molecular Plant

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

(2008) X. Li et al.   PLANT CELL

Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks

(2008) Ana Pilar Ortega-Galisteo et al.   PLANT MOLECULAR BIOLOGY

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)

(2008) C. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development

(2008) Q. Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana

(2008) Jixian Zhai et al.   PLoS Genetics