Importance of DNA and histone methylation inin vitroplant propagation for crop improvement: a review

Somatic embryogenesis — Stress-induced remodeling of plant cell fate

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

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2015) Meilina Ong-Abdullah et al.   NATURE

DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance inArabidopsis

(2015) Xuehua Zhong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Involvement of DNA methylation in the control of cell growth during heat stress in tobacco BY-2 cells

(2015) Isabella Centomani et al.   PROTOPLASMA

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

Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

(2014) Scott C. Stelpflug et al.   GENETICS

Environmentally responsive genome-wide accumulation of de novoArabidopsis thalianamutations and epimutations

(2014) Caifu Jiang et al.   GENOME RESEARCH

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

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

A Comprehensive View of the Epigenetic Landscape. Part II: Histone Post-translational Modification, Nucleosome Level, and Chromatin Regulation by ncRNAs

(2014) Anna Sadakierska-Chudy et al.   NEUROTOXICITY RESEARCH

DNA methylation changes in triticale due to in vitro culture plant regeneration and consecutive reproduction

(2014) Joanna Machczyńska et al.   PLANT CELL TISSUE AND ORGAN CULTURE

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

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

(2014) Takaki Yamauchi et al.   PLANT MOLECULAR BIOLOGY

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

(2014) Patrick T. West et al.   PLoS One

Transmission of Epi-Alleles with MET1-Dependent Dense Methylation in Arabidopsis thaliana

(2014) Michael Watson et al.   PLoS One

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

Assessment of DNA methylation changes in tissue culture of Brassica napus

(2014) Y. Gao et al.   RUSSIAN JOURNAL OF GENETICS

Over-expression of histone H3K4 demethylase gene JMJ15 enhances salt tolerance in Arabidopsis

(2014) Yuan Shen et al.   Frontiers in Plant Science

DNA methylation patterns and karyotype analysis of off-type and normal phenotype somatic embryos of feijoa

(2014) Caroline Cristofolini et al.   Theoretical and Experimental Plant Physiology

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

(2013) Hume Stroud et al.   CELL

Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture

(2013) Kateřina Křížová et al.   Epigenetics

Genome-Wide Analysis of DNA Methylation in Soybean

(2013) Qing-Xin Song et al.   Molecular Plant

Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes

(2013) Chad E. Niederhuth et al.   Molecular Plant

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

(2013) I. Makarevitch et al.   PLANT CELL

Wuschel overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro

(2013) O. Bouchabké-Coussa et al.   PLANT CELL REPORTS

High Genetic and Epigenetic Stability in Coffea arabica Plants Derived from Embryogenic Suspensions and Secondary Embryogenesis as Revealed by AFLP, MSAP and the Phenotypic Variation Rate

(2013) Roberto Bobadilla Landey et al.   PLoS One

Genome-Wide Quantitative Identification of DNA Differentially Methylated Sites in Arabidopsis Seedlings Growing at Different Water Potential

(2013) Alejandro C. Colaneri 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

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

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

Plants regenerated from tissue culture contain stable epigenome changes in rice

(2013) Hume Stroud et al.   eLife

Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation

(2012) Stéphanie Durand et al.   CURRENT BIOLOGY

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

Developmental silencing of the AtTERT gene is associated with increased H3K27me3 loading and maintenance of its euchromatic environment

(2012) Anna Ogrocká et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Assessment of genetic and epigenetic variation during long-term Taxus cell culture

(2012) Chunhua Fu 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

Involvement of DNA methylation in the regulation of STS10 gene expression in Vitis amurensis

(2012) Konstantin V. Kiselev et al.   PLANTA

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

Epigenetics and crop improvement

(2012) Nathan M. Springer   TRENDS IN GENETICS

Epialleles in plant evolution

(2012) Detlef Weigel et al.   GENOME BIOLOGY

Histone variants and chromatin assembly in plant abiotic stress responses

(2011) Yan Zhu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Arabidopsis thaliana in vitro shoot regeneration is impaired by silencing of TIR1

(2011) M. Qiao et al.   BIOLOGIA PLANTARUM

The AP2/ERF Transcription Factor WIND1 Controls Cell Dedifferentiation in Arabidopsis

(2011) Akira Iwase et al.   CURRENT BIOLOGY

An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond

(2011) C. Miguel et al.   JOURNAL OF EXPERIMENTAL BOTANY

Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications

(2011) Anjanasree K. Neelakandan et al.   PLANT CELL REPORTS

From nucleosome to chromosome: a dynamic organization of genetic information

(2011) Paul Fransz et al.   PLANT JOURNAL

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

Histone Methylation in Higher Plants

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

Acclimatization of tissue cultured plantlets: from laboratory to land

(2010) Sheela Chandra et al.   BIOTECHNOLOGY LETTERS

Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation

(2010) Angelique Deleris et al.   EMBO REPORTS

Degrees make all the difference: The multifunctionality of histone H4 lysine 20 methylation

(2010) Yu Wang et al.   Epigenetics

Tissue Culture-Induced Novel Epialleles of a Myb Transcription Factor Encoded by pericarp color1 in Maize

(2010) Y. Rhee et al.   GENETICS

Transgenerational Inheritance and Resetting of Stress-Induced Loss of Epigenetic Gene Silencing in Arabidopsis

(2010) Christina Lang-Mladek et al.   Molecular Plant

OsSPL14 promotes panicle branching and higher grain productivity in rice

(2010) Kotaro Miura et al.   NATURE GENETICS

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

(2010) Ales Pecinka et al.   PLANT CELL

Somaclonal variation in plants: causes and detection methods

(2010) Michael W. Bairu et al.   PLANT GROWTH REGULATION

Putative Arabidopsis Transcriptional Adaptor Protein (PROPORZ1) is required to modulate histone acetylation in response to auxin

(2010) J. M. Anzola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stress-Induced Activation of Heterochromatic Transcription

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

Histone modification patterns and epigenetic codes

(2009) Andreas Lennartsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Variations in DNA methylation, acetylated histone H4, and methylated histone H3 during Pinus radiata needle maturation in relation to the loss of in vitro organogenic capability

(2009) Luis Valledor et al.   JOURNAL OF PLANT PHYSIOLOGY

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

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

(2009) Agnieszka Ledwoń et al.   PLANT CELL REPORTS

Epigenetic interplay between histone modifications and DNA methylation in gene silencing

(2008) T VAISSIERE et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

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

The MADS-Domain Transcriptional Regulator AGAMOUS-LIKE15 Promotes Somatic Embryo Development in Arabidopsis and Soybean

(2008) D. Thakare et al.   PLANT PHYSIOLOGY

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

(2008) Yana V. Bernatavichute et al.   PLoS One

Promoter DNA Hypermethylation and Gene Repression in Undifferentiated Arabidopsis Cells

(2008) María Berdasco et al.   PLoS One

Epigenomic Consequences of Immortalized Plant Cell Suspension Culture

(2008) Milos Tanurdzic et al.   PLOS BIOLOGY