Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

(2020) Anna M. Wójcik et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

(2020) Barbara Wójcikowska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

(2020) Xiaoping Xu et al.   Scientific Reports

The MADS-box transcription factor CmAGL11 modulates somatic embryogenesis in Chinese chestnut (Castanea mollissima Blume)

(2020) Yue-rong GAO et al.   Journal of Integrative Agriculture

Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome

(2020) Nino A. Espinas et al.   PLoS Genetics

Universality of the DNA methylation codes in Eucaryotes

(2019) Benoît Aliaga et al.   Scientific Reports

A Role for Epigenetic Regulation in the Adaptation and Stress Responses of Non-model Plants

(2019) Flávia Thiebaut et al.   Frontiers in Plant Science

Global Methylomic and Transcriptomic Analyses Reveal the Broad Participation of DNA Methylation in Daily Gene Expression Regulation of Populus trichocarpa

(2019) Lixiong Liang et al.   Frontiers in Plant Science

Antagonistic actions of FPA and IBM2 regulate transcript processing from genes containing heterochromatin

(2019) Aurélie Deremetz et al.   PLANT PHYSIOLOGY

Callus, Dedifferentiation, Totipotency, Somatic Embryogenesis: What These Terms Mean in the Era of Molecular Plant Biology?

(2019) Attila Fehér   Frontiers in Plant Science

Analysis of DNA Methylation Patterns Associated with In Vitro Propagated Globe Artichoke Plants Using an EpiRADseq-Based Approach

(2019) Elisa Cerruti et al.   Genes

Epigenetic Regulation of Plant Gametophyte Development

(2019) Vasily V. Ashapkin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptome dynamics of cork oak (Quercus suber) somatic embryogenesis reveals active gene players in transcription regulation and phytohormone homeostasis of embryo development

(2019) Tiago Capote et al.   Tree Genetics & Genomes

Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression

(2019) Adam J. Bewick et al.   G3-Genes Genomes Genetics

Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean

(2019) Lexiang Ji et al.   PLANT CELL

The explant developmental stage profoundly impacts small RNA-mediated regulation at the dedifferentiation step of maize somatic embryogenesis

(2019) Vasti T. Juárez-González et al.   Scientific Reports

Transcriptome analysis of the induction of somatic embryogenesis in Coffea canephora and the participation of ARF and Aux/IAA genes

(2019) Ana O. Quintana-Escobar et al.   PeerJ

Epigenetic Regulation of Auxin Homeostasis

(2019) Eduardo Mateo-Bonmatí et al.   Biomolecules

DNA methylation directs microRNA biogenesis in mammalian cells

(2019) Ohad Glaich et al.   Nature Communications

Exploring the relationship between intron retention and chromatin accessibility in plants

(2018) Fahad Ullah et al.   BMC GENOMICS

Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

(2018) Mahmoud W. Yaish et al.   BMC GENOMICS

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

(2018) Satoshi Takahashi et al.   DNA RESEARCH

Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres

(2018) Moaine El Baidouri et al.   Molecular Plant

Dynamics and function of DNA methylation in plants

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

Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation (SRA) process

(2018) Jianying Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

(2018) Daria Grzybkowska et al.   PLANT GROWTH REGULATION

Expression of heterologous lycopene β-cyclase gene in flax can cause silencing of its endogenous counterpart by changes in gene-body methylation and in ABA homeostasis mechanism

(2018) Aleksandra Boba et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species

(2018) Dafni Anastasiadi et al.   Epigenetics & Chromatin

Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells

(2018) Junko Hasegawa et al.   Scientific Reports

Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea

(2018) Himanshi Bhatia et al.   Scientific Reports

DNA-Methylation: Master or Slave of Neural Fate Decisions?

(2018) Stefan H. Stricker et al.   Frontiers in Neuroscience

Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf.

(2018) Rezaul Karim et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Trichostatin A Triggers an Embryogenic Transition in Arabidopsis Explants via an Auxin-Related Pathway

(2018) Barbara Wójcikowska et al.   Frontiers in Plant Science

The role of miRNA in somatic embryogenesis

(2018) Zahid Hameed Siddiqui et al.   GENOMICS

5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis

(2018) Pedro Osorio-Montalvo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deciphering Auxin-Ethylene Crosstalk at a Systems Level

(2018) Elena V. Zemlyanskaya et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DNA Methylation and the Evolution of Developmental Complexity in Plants

(2018) Katharina Bräutigam et al.   Frontiers in Plant Science

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

(2017) Jidi Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis

(2017) Barbara Wójcikowska et al.   PLANT CELL REPORTS

Epigenetics of long-term somatic embryogenesis in Theobroma cacao L.: DNA methylation and recovery of embryogenic potential

(2017) Liliana Alexandra Pila Quinga et al.   PLANT CELL TISSUE AND ORGAN CULTURE

The BABY BOOM transcription factor activates the LEC1-ABI3-FUS3-LEC2 network to induce somatic embryogenesis

(2017) Anneke Horstman et al.   PLANT PHYSIOLOGY

Regulation of seedling growth by ethylene and the ethylene–auxin crosstalk

(2017) Yuming Hu et al.   PLANTA

PRC2 Represses Hormone-Induced Somatic Embryogenesis in Vegetative Tissue of Arabidopsis thaliana

(2017) Iva Mozgová et al.   PLoS Genetics

Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants

(2017) Ana M. Fortes et al.   Frontiers in Plant Science

miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis

(2017) Anna M. Wójcik et al.   Frontiers in Plant Science

MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis

(2017) Katarzyna Szyrajew et al.   Frontiers in Plant Science

The association between DNA methylation and exon expression in the Pacific oyster Crassostrea gigas

(2017) Kai Song et al.   PLoS One

Dynamic Changes of Genome-Wide DNA Methylation during Soybean Seed Development

(2017) Yong-qiang Charles An et al.   Scientific Reports

Transcriptional Responses to the Auxin Hormone

(2016) Dolf Weijers et al.   Annual Review of Plant Biology

De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.)

(2016) Xueping Shi et al.   BMC GENOMICS

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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

Chromatin-Based Epigenetic Regulation of Plant Abiotic Stress Response

(2016) Garima Pandey et al.   CURRENT GENOMICS

Parental epigenetic asymmetry of PRC2‐mediated histone modifications in theArabidopsisendosperm

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

Water-deficiency conditions differently modulate the methylome of roots and leaves in barley (Hordeum vulgareL.)

(2016) Karolina Chwialkowska et al.   JOURNAL OF EXPERIMENTAL BOTANY

Epigenetic Modifications and Plant Hormone Action

(2016) Chizuko Yamamuro et al.   Molecular Plant

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

(2016) Xutong Wang et al.   Molecular Plant

Transcription factors as readers and effectors of DNA methylation

(2016) Heng Zhu et al.   NATURE REVIEWS GENETICS

Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium

(2016) Sheng Jun Feng et al.   PLANT CELL AND ENVIRONMENT

Gene Regulation by the AGL15 Transcription Factor Reveals Hormone Interactions in Somatic Embryogenesis

(2016) Qiaolin Zheng et al.   PLANT PHYSIOLOGY

On the origin and evolutionary consequences of gene body DNA methylation

(2016) Adam J. Bewick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies

(2016) Yuvraj Indoliya et al.   Scientific Reports

DNA methylation changes and TE activity induced in tissue cultures of barley (Hordeum vulgare L.)

(2016) Renata Orłowska et al.   Journal of Biological Research-Thessaloniki

Somatic embryogenesis — Stress-induced remodeling of plant cell fate

(2015) Attila Fehér   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Epigenetic and hormonal profile during maturation of Quercus Suber L. somatic embryos

(2015) Marta Pérez et al.   JOURNAL OF PLANT PHYSIOLOGY

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

(2015) Meilina Ong-Abdullah et al.   NATURE

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Modeling the relationship of epigenetic modifications to transcription factor binding

(2015) Liang Liu et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

Inverted-Repeat RNAs TargetingFTIntronic Regions PromoteFTExpression in Arabidopsis

(2015) Shulin Deng et al.   PLANT AND CELL PHYSIOLOGY

DRM1 and DRM2 are involved in Arabidopsis callus formation

(2015) Fangwei Jiang et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Keeping the gate closed: functions of the polycomb repressive complex PRC2 in development

(2015) Iva Mozgova et al.   PLANT JOURNAL

DNA Methylation within Transcribed Regions

(2015) Taiko K. To et al.   PLANT PHYSIOLOGY

Ethylene and Hormonal Cross Talk in Vegetative Growth and Development

(2015) Bram Van de Poel et al.   PLANT PHYSIOLOGY

Methylation-Sensitive Expression of a DNA Demethylase Gene Serves As an Epigenetic Rheostat

(2015) Ben P. Williams et al.   PLoS Genetics

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

(2015) Manu J Dubin et al.   eLife

The age-dependent epigenetic and physiological changes in an Arabidopsis T87 cell suspension culture during long-term cultivation

(2014) Aleksandra Kwiatkowska et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress

(2014) Dan Liang et al.   BMC GENETICS

Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis

(2014) Hongxing Yang et al.   PLANT JOURNAL

ERF022 impacts the induction of somatic embryogenesis in Arabidopsis through the ethylene-related pathway

(2014) Katarzyna Nowak et al.   PLANTA

Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

(2013) Kelly Vining et al.   BMC PLANT BIOLOGY

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants

(2013) SUSHIL KUMAR et al.   JOURNAL OF GENETICS

In search of markers for somatic embryo maturation in hybrid larch (Larix×eurolepis): global DNA methylation and proteomic analyses

(2013) Caroline Teyssier et al.   PHYSIOLOGIA PLANTARUM

Global DNA methylation profiles of somatic embryos of peach palm (Bactris gasipaes Kunth) are influenced by cryoprotectants and droplet-vitrification cryopreservation

(2013) Angelo S. Heringer et al.   PLANT CELL TISSUE AND ORGAN CULTURE

LEAFY COTYLEDON2 (LEC2) promotes embryogenic induction in somatic tissues of Arabidopsis, via YUCCA-mediated auxin biosynthesis

(2013) Barbara Wójcikowska et al.   PLANTA

Extensive Modulation of the Transcription Factor Transcriptome during Somatic Embryogenesis in Arabidopsis thaliana

(2013) Marta Gliwicka et al.   PLoS One

New Insights into Somatic Embryogenesis: LEAFY COTYLEDON1, BABY BOOM1 and WUSCHEL-RELATED HOMEOBOX4 Are Epigenetically Regulated in Coffea canephora

(2013) Geovanny I. Nic-Can et al.   PLoS One

RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1

(2013) X. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immature Zygotic Embryo Cultures of Arabidopsis. A Model System for Molecular Studies on Morphogenic Pathways Induced In Vitro

(2012) Małgorzata Kraut et al.   ACTA BIOLOGICA CRACOVIENSIA SERIES BOTANICA

Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

(2012) Xiyan Yang et al.   BMC PLANT BIOLOGY

DNA Methylation Dynamics during Sexual Reproduction in Arabidopsis thaliana

(2012) Pauline E. Jullien et al.   CURRENT BIOLOGY

Induction of Somatic Embryos in Arabidopsis Requires Local YUCCA Expression Mediated by the Down-Regulation of Ethylene Biosynthesis

(2012) Bo Bai et al.   Molecular Plant

5-Azacytidine combined with 2,4-D improves somatic embryogenesis of Acca sellowiana (O. Berg) Burret by means of changes in global DNA methylation levels

(2012) Hugo P. F. Fraga et al.   PLANT CELL REPORTS

Variations in genomic DNA methylation during the long-term in vitro proliferation of oil palm embryogenic suspension cultures

(2012) Alain Rival et al.   PLANT CELL REPORTS

The Dynamic Changes of DNA Methylation and Histone Modifications of Salt Responsive Transcription Factor Genes in Soybean

(2012) Yuguang Song et al.   PLoS One

Mechanisms that impact microRNA stability in plants

(2012) Yuanyuan Zhao et al.   RNA Biology

Auxin and ethylene: collaborators or competitors?

(2012) Gloria K. Muday et al.   TRENDS IN PLANT SCIENCE

Epigenetic control of gene regulation in plants

(2011) Massimiliano Lauria et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Chromatin Reprogramming: Gender Equality during Arabidopsis Germline Differentiation

(2011) Yannick Jacob et al.   CURRENT BIOLOGY

Synergistic repression of the embryonic programme by SET DOMAIN GROUP 8 and EMBRYONIC FLOWER 2 in Arabidopsis seedlings

(2011) Xurong Tang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expression of seed storage product genes (CRA1 and OLEO4) in embryogenic cultures of somatic tissues of Arabidopsis

(2011) Marta Gliwicka et al.   PLANT CELL TISSUE AND ORGAN CULTURE

LEAFY COTYLEDON1, FUSCA3 expression and auxin treatment in relation to somatic embryogenesis induction in Arabidopsis

(2011) Agnieszka Ledwoń et al.   PLANT GROWTH REGULATION

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

(2011) Fabienne Brenet et al.   PLoS One

DNA Methylation and Histone Modifications Regulate De Novo Shoot Regeneration in Arabidopsis by Modulating WUSCHEL Expression and Auxin Signaling

(2011) Wei Li et al.   PLoS Genetics

Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex

(2010) Assaf Zemach et al.   CURRENT BIOLOGY

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Arabidopsis EMBRYOMAKER encoding an AP2 domain transcription factor plays a key role in developmental change from vegetative to embryonic phase

(2010) Ryo Tsuwamoto et al.   PLANT MOLECULAR BIOLOGY

Phylogeny of Methylomes

(2010) A. Jeltsch   SCIENCE

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

Genome-scale DNA methylation analysis

(2010) Shaun D Fouse et al.   Epigenomics

Mechanism of Auxin-Regulated Gene Expression in Plants

(2009) Elisabeth J. Chapman et al.   Annual Review of Genetics

Possible involvement of DNA methylation on expression regulation of carrot LEC1 gene in its 5′-upstream region

(2009) Tomiko Shibukawa et al.   GENE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

LEAFY COTYLEDON2 gene expression and auxin treatment in relation to embryogenic capacity of Arabidopsis somatic cells

(2009) Agnieszka Ledwoń et al.   PLANT CELL REPORTS

AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation

(2009) Mahmoud W. F. Yaish et al.   PLANT JOURNAL

Auxin-inducedWUSexpression is essential for embryonic stem cell renewal during somatic embryogenesis in Arabidopsis

(2009) Ying H. Su et al.   PLANT JOURNAL

Cytokinin and WUSCHEL tie the knot around plant stem cells

(2009) R. Sablowski   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

(2008) Felipe F Aceituno et al.   BMC GENOMICS

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

(2008) Ryan Lister et al.   CELL

Biological characterization of young and aged embryogenic cultures of Pinus pinaster (Ait.)

(2008) K. Klimaszewska et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT

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

Promoter DNA Hypermethylation and Gene Repression in Undifferentiated Arabidopsis Cells

(2008) María Berdasco et al.   PLoS One

LECs go crazy in embryo development

(2008) S BRAYBROOK et al.   TRENDS IN PLANT SCIENCE