Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location

Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon

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Monitoring the interplay between transposable element families and DNA methylation in maize

(2019) Jaclyn M. Noshay et al.   PLoS Genetics

Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions

(2018) Kenta Nakashima et al.   CHROMOSOME RESEARCH

Transcription of soybean retrotransposon SORE-1 is temporally upregulated in developing ovules

(2018) Kenta Nakashima et al.   PLANTA

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice

(2017) Jae Young Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA silencing in the life cycle of soybean: multiple restriction systems and spatiotemporal variation associated with plant architecture

(2017) Ayumi Mori et al.   TRANSGENIC RESEARCH

A recessive allele for delayed flowering at the soybean maturity locus E9 is a leaky allele of FT2a, a FLOWERING LOCUS T ortholog

(2016) Chen Zhao et al.   BMC PLANT BIOLOGY

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

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

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

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

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

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

(2015) Kyung Do Kim et al.   PLANT PHYSIOLOGY

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

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

Natural occurring epialleles determine vitamin E accumulation in tomato fruits

(2014) Leandro Quadrana et al.   Nature Communications

Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia

(2013) Megumi Kasai et al.   BMC GENOMICS

Widespread, abundant, and diverse TE-associated siRNAs in developing wheat grain

(2013) Fenglong Sun et al.   GENE

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs

(2013) S. Nuthikattu et al.   PLANT PHYSIOLOGY

Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin

(2013) Hidetoshi Saze et al.   Nature Communications

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

(2012) Douglas S Domingues et al.   BMC GENOMICS

Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

(2012) A. T. Wierzbicki et al.   GENES & DEVELOPMENT

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

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

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

(2012) Steven R. Eichten et al.   PLoS Genetics

Size and positional effects of promoter RNA segments on virus-induced RNA-directed DNA methylation and transcriptional gene silencing

(2011) Shungo Otagaki et al.   Epigenetics

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

(2011) Megumi Kasai et al.   PLANT MOLECULAR BIOLOGY

Small RNAs, DNA methylation and transposable elements in wheat

(2010) Dario Cantu et al.   BMC GENOMICS

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

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

Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison

(2010) Jianchang Du et al.   PLANT JOURNAL

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Endogenous short interfering RNAs of chalcone synthase genes associated with inhibition of seed coat pigmentation in soybean

(2009) Tasuku Kurauchi et al.   BREEDING SCIENCE

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

Adaptive Evolution Involving Gene Duplication and Insertion of a Novel Ty1/copia-Like Retrotransposon in Soybean

(2009) Akira Kanazawa et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2009) Antoine Martin et al.   NATURE

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis

(2009) Xiaopeng Qi et al.   PLoS One

Distinct extremely abundant siRNAs associated with cosuppression in petunia

(2009) E. De Paoli et al.   RNA

Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading

(2008) I. R. Henderson et al.   GENES & DEVELOPMENT

Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene

(2008) B. Liu et al.   GENETICS

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

A structural-maintenance-of-chromosomes hinge domain–containing protein is required for RNA-directed DNA methylation

(2008) Tatsuo Kanno et al.   NATURE GENETICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

(2008) K. Nobuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA