Factor of DNA methylation 1 affects woodland strawberry plant stature and organ size via DNA methylation

Spatial control of cell division by GA‐OsGRF7/8 module in a leaf explains the leaf length variation between cultivated and wild rice

(2022) Vikram Jathar et al.   NEW PHYTOLOGIST

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

(2021) Kezhi Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements

(2020) Le Xu et al.   Molecular Plant

Transposon age and non-CG methylation

(2020) Zhengming Wang et al.   Nature Communications

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

A 1.7‐Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach

(2020) Hui Zhou et al.   PLANT BIOTECHNOLOGY JOURNAL

Updated annotation of the wild strawberry Fragaria vesca V4 genome

(2019) Yongping Li et al.   Horticulture Research

Conserved and novel roles of miR164‐ CUC 2 regulatory module in specifying leaf and floral organ morphology in strawberry

(2019) Guanghui Zheng et al.   NEW PHYTOLOGIST

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Reduced Anthocyanins in Petioles codes for a GST anthocyanin transporter that is essential for the foliage and fruit coloration in strawberry

(2018) Huifeng Luo et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dynamics and function of DNA methylation in plants

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

Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants

(2018) Shira Corem et al.   PLANT CELL

OsMADS6Controls Flower Development by Activating RiceFACTOR OF DNA METHYLATION LIKE1

(2018) Juhong Tao et al.   PLANT PHYSIOLOGY

Reporter gene expression reveals precise auxin synthesis sites during fruit and root development in wild strawberry

(2018) Jia Feng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Interlinked regulatory loops of ABA catabolism and biosynthesis coordinate fruit growth and ripening in woodland strawberry

(2018) Xiong Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A common genetic mechanism underlies morphological diversity in fruits and other plant organs

(2018) Shan Wu et al.   Nature Communications

Development and Validation of an Effective CRISPR/Cas9 Vector for Efficiently Isolating Positive Transformants and Transgene-Free Mutants in a Wide Range of Plant Species

(2018) Ting Tang et al.   Frontiers in Plant Science

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

(2017) Zhaobo Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

(2017) Patrick P Edger et al.   GigaScience

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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

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

(2016) Feng Tan et al.   PLANT PHYSIOLOGY

DNA Methylation Signatures of the Plant Chromomethyltransferases

(2016) Quentin Gouil et al.   PLoS Genetics

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

(2015) Chaoyang Cheng et al.   PLANT JOURNAL

A DEMETER-like DNA demethylase governs tomato fruit ripening

(2015) Ruie Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

Expression analysis of Arabidopsis XH/XS-domain proteins indicates overlapping and distinct functions for members of this gene family

(2014) Haroon Butt et al.   JOURNAL OF EXPERIMENTAL BOTANY

CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants

(2014) Yang Lei et al.   Molecular Plant

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

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

RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA

(2014) Gudrun Böhmdorfer 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

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

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(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Assaf Zemach et al.   CELL

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

(2013) Hume Stroud et al.   CELL

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

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca

(2013) C. Kang et al.   PLANT CELL

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Small RNAs and heritable epigenetic variation in plants

(2013) Donna M. Bond et al.   TRENDS IN CELL BIOLOGY

IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation

(2012) Andreas Finke et al.   Epigenetics

A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation

(2012) Meng Xie et al.   NUCLEIC ACIDS RESEARCH

FaGAST2, a Strawberry Ripening-Related Gene, Acts Together with FaGAST1 to Determine Cell Size of the Fruit Receptacle

(2012) Enriqueta Moyano-Cañete et al.   PLANT AND CELL PHYSIOLOGY

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 DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation

(2012) Meng Xie et al.   PLANT JOURNAL

INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

(2012) I. Ausin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IDN2 and Its Paralogs Form a Complex Required for RNA–Directed DNA Methylation

(2012) Cui-Jun Zhang et al.   PLoS Genetics

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

Plant Aurora kinases play a role in maintenance of primary meristems and control of endoreduplication

(2011) Beáta Petrovská et al.   NEW PHYTOLOGIST

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

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

An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis

(2010) Zhimin Zheng et al.   PLANT JOURNAL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana

(2009) Israel Ausin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Control of final seed and organ size by the DA1 gene family in Arabidopsis thaliana

(2008) Y. Li et al.   GENES & DEVELOPMENT

The Plant TPX2 Protein Regulates Prospindle Assembly before Nuclear Envelope Breakdown

(2008) J. W. Vos et al.   PLANT CELL