A role for palindromic structures in the cis -region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response

LTR retrotransposons, handy hitchhikers of plant regulation and stress response

(2015) Marie-Angèle Grandbastien   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Silencing of active transposable elements in plants

(2015) Dalen Fultz et al.   CURRENT OPINION IN PLANT BIOLOGY

The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs inArabidopsis

(2014) Nicolas G. Bologna et al.   Annual Review of Plant Biology

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation

(2014) A. D. McCue et al.   EMBO JOURNAL

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

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

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

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

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

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

(2014) Concepcion M. Diez et al.   PLoS Genetics

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

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

(2013) Assaf Zemach et al.   CELL

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

(2013) S. Takuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Arguments for standardizing transposable element annotation in plant genomes

(2013) Raja Ragupathy et al.   TRENDS IN PLANT SCIENCE

Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world

(2013) Alexandros Bousios et al.   Mobile DNA

MASiVEdb: the Sirevirus Plant Retrotransposon Database

(2012) Alexandros Bousios et al.   BMC GENOMICS

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

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

Repeat associated small RNAs vary among parents and following hybridization in maize

(2012) W. T. Barber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story

(2011) Alexandros Bousios et al.   PLANT JOURNAL

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences

(2010) N. Darzentas et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BS Seeker: precise mapping for bisulfite sequencing

(2010) Pao-Yang Chen et al.   BMC BIOINFORMATICS

Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?

(2010) Alexandros Bousios et al.   BMC GENOMICS

Small RNAs, DNA methylation and transposable elements in wheat

(2010) Dario Cantu et al.   BMC GENOMICS

Patching gaps in plant genomes results in gene movement and erosion of colinearity

(2010) T. Wicker et al.   GENOME RESEARCH

Bifurcation and Enhancement of Autonomous-Nonautonomous Retrotransposon Partnership through LTR Swapping in Soybean

(2010) J. Du et al.   PLANT CELL

Epigenetic reprogramming during vegetative phase change in maize

(2010) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang et al.   PLANT CELL

A Role for RNAi in the Selective Correction of DNA Methylation Defects

(2009) F. K. Teixeira et al.   SCIENCE

A Genome-Wide Characterization of MicroRNA Genes in Maize

(2009) Lifang Zhang et al.   PLoS Genetics

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

(2008) Ryan Lister et al.   CELL

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Sustained retrotransposition is mediated by nucleotide deletions and interelement recombinations

(2008) A. Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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