Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation

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

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

Flood adaptive traits and processes: an overview

(2015) Laurentius A. C. J. Voesenek et al.   NEW PHYTOLOGIST

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

(2015) Chaoyang Cheng et al.   PLANT JOURNAL

Mechanisms of growth and patterns of gene expression in oxygen-deprived rice coleoptiles

(2015) Reena Narsai et al.   PLANT JOURNAL

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

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

A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice

(2015) Tobias Kretzschmar et al.   Nature Plants

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

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

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

(2014) Takaki Yamauchi et al.   PLANT MOLECULAR BIOLOGY

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

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

(2013) Assaf Zemach et al.   CELL

Low Oxygen Response Mechanisms in Green Organisms

(2013) Valeria Banti et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Ethylene - and oxygen signalling - drive plant survival during flooding

(2013) L. A. C. J. Voesenek et al.   PLANT BIOLOGY

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

(2013) D. Secco et al.   PLANT CELL

Rice DB: anOryzaInformation Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis

(2013) Reena Narsai et al.   PLANT JOURNAL

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Characterization of the Phosphofructokinase Gene Family in Rice and Its Expression Under Oxygen Deficiency Stress

(2013) Angelika Mustroph et al.   Frontiers in Plant Science

How unique is the low oxygen response? An analysis of the anaerobic response during germination and comparison with abiotic stress in rice and Arabidopsis

(2013) Reena Narsai et al.   Frontiers in Plant Science

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

(2012) Jiamu Du et al.   CELL

Quantifying ATP turnover in anoxic coleoptiles of rice (Oryza sativa) demonstrates preferential allocation of energy to protein synthesis

(2012) Joshua M. Edwards et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

The Submergence Tolerance Gene SUB1A Delays Leaf Senescence under Prolonged Darkness through Hormonal Regulation in Rice

(2012) T. Fukao et al.   PLANT PHYSIOLOGY

Reactive Oxygen Species-Driven Transcription in Arabidopsis under Oxygen Deprivation

(2012) C. Pucciariello et al.   PLANT PHYSIOLOGY

Making sense of low oxygen sensing

(2012) Julia Bailey-Serres et al.   TRENDS IN PLANT SCIENCE

Cell division and cell elongation in the coleoptile of rice alcohol dehydrogenase 1-deficient mutant are reduced under complete submergence

(2011) Hirokazu Takahashi et al.   ANNALS OF BOTANY

Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants

(2011) Daniel J. Gibbs et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Differential Molecular Responses of Rice and Wheat Coleoptiles to Anoxia Reveal Novel Metabolic Adaptations in Amino Acid Metabolism for Tissue Tolerance

(2011) R. N. Shingaki-Wells et al.   PLANT PHYSIOLOGY

HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana

(2010) Francesco Licausi et al.   PLANT JOURNAL

Arabidopsis RAP2.2: An Ethylene Response Transcription Factor That Is Important for Hypoxia Survival

(2010) M. Hinz et al.   PLANT PHYSIOLOGY

Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses

(2010) A. Mustroph et al.   PLANT PHYSIOLOGY

Oxidative metabolism, ROS and NO under oxygen deprivation

(2010) Olga Blokhina et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water

(2009) Yoko Hattori et al.   NATURE

Anoxic nitric oxide cycling in plants: participating reactions and possible mechanisms

(2009) Abir U. Igamberdiev et al.   PHYSIOLOGIA PLANTARUM

Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice

(2009) Haiyan Ye et al.   PLANT MOLECULAR BIOLOGY

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings

(2009) R. Narsai et al.   PLANT PHYSIOLOGY

Rice germination and seedling growth in the absence of oxygen

(2008) Leonardo Magneschi et al.   ANNALS OF BOTANY

Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process

(2008) K. A. Howell et al.   PLANT PHYSIOLOGY

Does anoxia tolerance involve altering the energy currency towards PPi?

(2008) Shaobai Huang et al.   TRENDS IN PLANT SCIENCE