Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprograming of Defense Responses in Plants

The Tug-of-War between Plants and Viruses: Great Progress and Many Remaining Questions

(2019) Xiaoyun Wu et al.   Viruses-Basel

Perception of double‐stranded RNA in plant antiviral immunity

(2019) Annette Niehl et al.   MOLECULAR PLANT PATHOLOGY

Virus perception at the cell surface: revisiting the roles of receptor‐like kinases as viral pattern recognition receptors

(2019) Ruan M. Teixeira et al.   MOLECULAR PLANT PATHOLOGY

DNA Methylation Analysis of the Citrullus lanatus Response to Cucumber Green Mottle Mosaic Virus Infection by Whole-Genome Bisulfite Sequencing

(2019) Sun et al.   Genes

Crosstalk between epigenetic silencing and infection by tobacco rattle virus in Arabidopsis

(2019) Laura Diezma‐Navas et al.   MOLECULAR PLANT PATHOLOGY

The Histone Demethylase IBM1 Positively Regulates Arabidopsis Immunity by Control of Defense Gene Expression

(2019) Ching Chan et al.   Frontiers in Plant Science

Transcriptional control and exploitation of an immune‐responsive family of plant retrotransposons

(2018) Jérôme Zervudacki et al.   EMBO JOURNAL

Arabidopsis RNA Polymerase V Mediates Enhanced Compaction and Silencing of Geminivirus and Transposon Chromatin during Host Recovery from Infection

(2018) Tami Coursey et al.   JOURNAL OF VIROLOGY

Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study

(2018) Héctor Cervera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Network modelling unravels mechanisms of crosstalk between ethylene and salicylate signalling in potato

(2018) Živa Ramšak et al.   PLANT PHYSIOLOGY

Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

(2018) Svenja Mager et al.   Frontiers in Plant Science

Epigenetic Changes in the Regulation of Nicotiana tabacum Response to Cucumber Mosaic Virus Infection and Symptom Recovery through Single-Base Resolution Methylomes

(2018) Chenguang Wang et al.   Viruses-Basel

Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways

(2017) Clément Lafon-Placette et al.   JOURNAL OF EXPERIMENTAL BOTANY

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

(2017) Runxuan Zhang et al.   NUCLEIC ACIDS RESEARCH

Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple

(2017) Jidi Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2017) Reena Narsai et al.   PLANT JOURNAL

The Potyvirus Silencing Suppressor Protein VPg Mediates Degradation of SGS3 via Ubiquitination and Autophagy Pathways

(2016) Xiaofei Cheng et al.   JOURNAL OF VIROLOGY

Epigenetic Mechanisms: An Emerging Player in Plant-Microbe Interactions

(2016) Qian-Hao Zhu et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants

(2016) Annette Niehl et al.   NEW PHYTOLOGIST

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

The role of DNA (de)methylation in immune responsiveness of Arabidopsis

(2016) Ana López Sánchez et al.   PLANT JOURNAL

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

(2016) Pooja Negi et al.   Frontiers in Plant Science

The transcriptomics of an experimentally evolved plant-virus interaction

(2016) Julia Hillung et al.   Scientific Reports

Effector-Triggered Immunity: From Pathogen Perception to Robust Defense

(2015) Haitao Cui et al.   Annual Review of Plant Biology

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues

(2015) R.R. Oliveira et al.   GENETICS AND MOLECULAR RESEARCH

Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns

(2015) Flora Sánchez et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulatory link between DNA methylation and active demethylation inArabidopsis

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

Viral quasispecies

(2015) Raul Andino et al.   VIROLOGY

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

(2015) David Secco et al.   eLife

Different roles for RNA silencing and RNA processing components in virus recovery and virus-induced gene silencing in plants

(2014) Xiaofang Ma et al.   JOURNAL OF EXPERIMENTAL BOTANY

Molecular and cellular mechanisms underlying potyvirus infection

(2014) K. I. Ivanov et al.   JOURNAL OF GENERAL VIROLOGY

Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors

(2014) A. Stief et al.   PLANT CELL

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

(2014) Danelle K. Seymour et al.   PLoS Genetics

Systemic Acquired Resistance: Turning Local Infection into Global Defense

(2013) Zheng Qing Fu et al.   Annual Review of Plant Biology

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

(2013) A. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thaliana

(2013) Maxim V. C. Greenberg et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns

(2012) Mélanie Rigal et al.   EMBO JOURNAL

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Next-Generation Systemic Acquired Resistance

(2011) E. Luna et al.   PLANT PHYSIOLOGY

The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity

(2011) Ana López et al.   PLoS Genetics

Viral Suppressors of RNA-Based Viral Immunity: Host Targets

(2010) Qingfa Wu et al.   Cell Host & Microbe

JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis

(2010) Falong Lu et al.   CELL RESEARCH

JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis

(2010) I. R. Searle et al.   GENES & DEVELOPMENT

Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress inArabidopsis

(2010) Ales Pecinka et al.   PLANT CELL

A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis

(2010) Wannian Yang et al.   PLANT JOURNAL

Stress-Induced Activation of Heterochromatic Transcription

(2010) Mireille Tittel-Elmer et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites

(2009) Asuka Miura et al.   EMBO JOURNAL

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense

(2008) K.-C. Kim et al.   PLANT CELL

Virus Adaptation by Manipulation of Host's Gene Expression

(2008) Patricia Agudelo-Romero et al.   PLoS One

Control of Genic DNA Methylation by a jmjC Domain-Containing Protein in Arabidopsis thaliana

(2008) H. Saze et al.   SCIENCE