Transposable Elements, Epigenetics, and Genome Evolution

Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata

(2012) S. Tsukahara et al.   GENES & DEVELOPMENT

Vernalization - a cold-induced epigenetic switch

(2012) J. Song et al.   JOURNAL OF CELL SCIENCE

Transposase-Derived Proteins FHY3/FAR1 Interact with PHYTOCHROME-INTERACTING FACTOR1 to Regulate Chlorophyll Biosynthesis by Modulating HEMB1 during Deetiolation in Arabidopsis

(2012) W. Tang et al.   PLANT CELL

Inter-species sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity

(2012) Jan P. Buchmann et al.   PLANT JOURNAL

The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression

(2012) Andriy Bilichak et al.   PLoS One

Nuclear DNA amounts in angiosperms: targets, trends and tomorrow

(2011) M. D. Bennett et al.   ANNALS OF BOTANY

Mutagenesis by imprecise excision of the piggyBac transposon in Drosophila melanogaster

(2011) Heuijong Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Epigenetics in plants—vernalisation and hybrid vigour

(2011) Michael Groszmann et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Cell cycle regulation of silent chromatin formation

(2011) Tiffany J. Young et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Adaptation to P Element Transposon Invasion in Drosophila melanogaster

(2011) Jaspreet S. Khurana et al.   CELL

Transposable element origins of epigenetic gene regulation

(2011) Damon Lisch et al.   CURRENT OPINION IN PLANT BIOLOGY

Selected aspects of transgenerational epigenetic inheritance and resetting in plants

(2011) Jerzy Paszkowski et al.   CURRENT OPINION IN PLANT BIOLOGY

RNA-directed DNA methylation

(2011) Huiming Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

Moving DNA around: DNA transposition and retroviral integration

(2011) Sherwin P Montaño et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The role of epigenetic processes in controlling flowering time in plants exposed to stress

(2011) M. W. Yaish et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Dynamic Gene Copy Number Variation in Collinear Regions of Grass Genomes

(2011) J.-H. Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rampant Horizontal Transfer of SPIN Transposons in Squamate Reptiles

(2011) C. Gilbert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inhibition of Homologous Recombination by the PCNA-Interacting Protein PARI

(2011) George-Lucian Moldovan et al.   MOLECULAR CELL

Modulation of AUXIN-BINDING PROTEIN 1 gene expression in maize and the teosintes by transposon insertions in its promoter

(2011) Nabil Elrouby et al.   MOLECULAR GENETICS AND GENOMICS

Abiotic stress leads to somatic and heritable changes in homologous recombination frequency, point mutation frequency and microsatellite stability in Arabidopsis plants

(2011) Youli Yao et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Local infection with oilseed rape mosaic virus promotes genetic rearrangements in systemic Arabidopsis tissue

(2011) Youli Yao et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II

(2011) Mikel Zaratiegui et al.   NATURE

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

(2011) Jeremy R. Haag et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives

(2011) Thomas Wicker et al.   PLANT CELL

Descendants of Primed Arabidopsis Plants Exhibit Resistance to Biotic Stress

(2011) A. Slaughter et al.   PLANT PHYSIOLOGY

Next-Generation Systemic Acquired Resistance

(2011) E. Luna et al.   PLANT PHYSIOLOGY

Telomerase and retrotransposons: Reverse transcriptases that shaped genomes

(2011) M. Belfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

(2011) N. Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies

(2011) Y.-W. Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SHH1, a Homeodomain Protein Required for DNA Methylation, As Well As RDR2, RDM4, and Chromatin Remodeling Factors, Associate with RNA Polymerase IV

(2011) Julie A. Law et al.   PLoS Genetics

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

DDE transposases: Structural similarity and diversity

(2010) Irina V. Nesmelova et al.   ADVANCED DRUG DELIVERY REVIEWS

Stc1: A Critical Link between RNAi and Chromatin Modification Required for Heterochromatin Integrity

(2010) Elizabeth H. Bayne et al.   CELL

Integrating prokaryotes and eukaryotes: DNA transposases in light of structure

(2010) Alison Burgess Hickman et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Paramutation in maize: RNA mediated trans-generational gene silencing

(2010) Mario Alberto Arteaga-Vazquez et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Differentiation of epigenetic modifications between transposons and genes

(2010) Hidetoshi Saze et al.   CURRENT OPINION IN PLANT BIOLOGY

Small RNA-mediated epigenetic modifications in plants

(2010) Stacey A Simon et al.   CURRENT OPINION IN PLANT BIOLOGY

Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response

(2010) Michal Jaskiewicz et al.   EMBO REPORTS

The epigenetic control of the Athila family of retrotransposons in Arabidopsis

(2010) R. Keith Slotkin   Epigenetics

DNA methylation systems and targets in plants

(2010) Peter Meyer   FEBS LETTERS

Pervasive Horizontal Transfer of Rolling-Circle Transposons among Animals

(2010) Jainy Thomas et al.   Genome Biology and Evolution

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

(2010) T. Wicker et al.   GENOME RESEARCH

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

(2010) Clément Gilbert et al.   NATURE

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

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

Transposases are the most abundant, most ubiquitous genes in nature

(2010) Ramy K. Aziz et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci

(2010) E. R. Havecker et al.   PLANT CELL

Small RNAs - secrets and surprises of the genome

(2010) Xuemei Chen   PLANT JOURNAL

Tobacco Mosaic Virus Infection Results in an Increase in Recombination Frequency and Resistance to Viral, Bacterial, and Fungal Pathogens in the Progeny of Infected Tobacco Plants

(2010) P. Kathiria et al.   PLANT PHYSIOLOGY

Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins

(2010) Alex Boyko et al.   PLoS One

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

Palaeogenomics of plants: synteny-based modelling of extinct ancestors

(2010) Michael Abrouk et al.   TRENDS IN PLANT SCIENCE

Gene Amplification and Adaptive Evolution in Bacteria

(2009) Dan I. Andersson et al.   Annual Review of Genetics

Active DNA Demethylation Mediated by DNA Glycosylases

(2009) Jian-Kang Zhu   Annual Review of Genetics

Transposable elements and an epigenetic basis for punctuated equilibria

(2009) David W. Zeh et al.   BIOESSAYS

On the need for widespread horizontal gene transfers under genome size constraint

(2009) Hervé Isambert et al.   Biology Direct

Transcriptional memory at the nuclear periphery

(2009) Jason H Brickner   CURRENT OPINION IN CELL BIOLOGY

Centromeres: long intergenic spaces with adaptive features

(2009) Lisa Kanizay et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

(2009) Z. Tian et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The polychromatic Helitron landscape of the maize genome

(2009) C. Du et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

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

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

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

CRISPR-based adaptive and heritable immunity in prokaryotes

(2009) John van der Oost et al.   TRENDS IN BIOCHEMICAL SCIENCES

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

(2009) Fusheng Wei et al.   PLoS Genetics

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

(2009) Sanzhen Liu et al.   PLoS Genetics

Epigenetic Regulation of Transposable Elements in Plants

(2008) Damon Lisch   Annual Review of Plant Biology

Mutational analysis of highly conserved aspartate residues essential to the catalytic core of the piggyBac transposase

(2008) James H Keith et al.   BMC MOLECULAR BIOLOGY

Epigenetic regulation of heterochromatic DNA stability

(2008) Jamy C Peng et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

(2008) R. S. Baucom et al.   GENOME RESEARCH

Enchilada redux: how complete is your genome sequence?

(2008) Renyi Liu et al.   NEW PHYTOLOGIST

Genomic imprinting: A balance between antagonistic roles of parental chromosomes

(2008) T KINOSHITA et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Origins and evolution of eukaryotic RNA interference

(2008) S SHABALINA et al.   TRENDS IN ECOLOGY & EVOLUTION