Chromatin structure and gene expression changes associated with loss of MOP1 activity inZea mays

Gene silencing in plants: A diversity of pathways

(2013) Angel Emilio Martínez de Alba et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2013) Hume Stroud et al.   CELL

Chromatin patterns associated with lung adenocarcinoma progression

(2013) Brooke Druliner et al.   CELL CYCLE

Changes in nucleosome position at transcriptional start sites of specific genes inZea mays mediator of paramutation1mutants

(2013) Jonathan D. J. Labonne et al.   Epigenetics

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

(2013) M. Regulski et al.   GENOME RESEARCH

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

Understanding the chromatin remodeling code

(2013) Misook Ha   PLANT SCIENCE

Revisiting RNA-directed DNA methylation

(2013) Athanasios Dalakouras et al.   RNA Biology

Enhancement of RNA-directed DNA methylation of a transgene by simultaneously downregulating a ROS1 ortholog using a virus vector in Nicotiana benthamiana

(2013) Shungo Otagaki et al.   Frontiers in Genetics

Methods for Identifying Higher-Order Chromatin Structure

(2012) Samin A. Sajan et al.   Annual Review of Genomics and Human Genetics

Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies

(2012) C. Smaczniak et al.   DEVELOPMENT

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

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

NERD, a Plant-Specific GW Protein, Defines an Additional RNAi-Dependent Chromatin-Based Pathway in Arabidopsis

(2012) Dominique Pontier et al.   MOLECULAR CELL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Roles of DICER-LIKE and ARGONAUTE Proteins in TAS-Derived Small Interfering RNA-Triggered DNA Methylation

(2012) L. Wu et al.   PLANT PHYSIOLOGY

Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis

(2012) X. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding

(2012) S.-i. Takebayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

RNA-directed DNA methylation

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

Identification of genes required for de novo DNA methylation in Arabidopsis

(2011) Maxim V.C. Greenberg et al.   Epigenetics

Genome-wide atlas of transcription during maize development

(2011) Rajandeep S. Sekhon et al.   PLANT JOURNAL

From nucleosome to chromosome: a dynamic organization of genetic information

(2011) Paul Fransz et al.   PLANT JOURNAL

Identification of Epigenetic Regulators of a Transcriptionally Silenced Transgene in Maize

(2011) Thelma F. Madzima et al.   G3-Genes Genomes Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Paramutation in maize: RNA mediated trans-generational gene silencing

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

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

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

The role of DNA methylation, nucleosome occupancy and histone modifications in paramutation

(2010) Max Haring et al.   PLANT JOURNAL

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

Chromatin Higher-order Structure and Dynamics

(2010) C. L. Woodcock et al.   Cold Spring Harbor Perspectives in Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

RNA Polymerase IV Functions in Paramutation in Zea mays

(2009) K. F. Erhard et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

AGAMOUS Controls GIANT KILLER, a Multifunctional Chromatin Modifier in Reproductive Organ Patterning and Differentiation

(2009) Kian-Hong Ng et al.   PLOS BIOLOGY

A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes

(2009) Lyudmila Sidorenko et al.   PLoS Genetics

Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

(2009) Yi Jia et al.   PLoS Genetics

Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

(2009) Jennifer L. Stonaker et al.   PLoS Genetics

Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis

(2008) Yukio Kurihara et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

RNA Silencing in Plants: Yesterday, Today, and Tomorrow

(2008) A. Eamens et al.   PLANT PHYSIOLOGY

Feminized tassels of maize mop1 and ts1 mutants exhibit altered levels of miR156 and specific SBP-box genes

(2008) Judd F. Hultquist et al.   PLANTA

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