4.8 Article

DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis

Javier Gallego-Bartolome et al.

Article Biochemistry & Molecular Biology

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq

Evan D. Tarbell et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition

Magdalena E. Potok et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation

Somsakul Pop Wongpalee et al.

NATURE COMMUNICATIONS (2019)

Article Plant Sciences

Widespread long-range cis-regulatory elements in the maize genome

William A. Ricci et al.

NATURE PLANTS (2019)

Article Biochemistry & Molecular Biology

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

Joachim Wolff et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis

Yu Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemistry & Molecular Biology

Transcription Elongation Can Affect Genome 3D Structure

Sven Heinz et al.

Article Genetics & Heredity

Links between DNA methylation and nucleosome occupancy in the human genome

Clayton K. Collings et al.

EPIGENETICS & CHROMATIN (2017)

Article Biotechnology & Applied Microbiology

The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana

Heike Wollmann et al.

GENOME BIOLOGY (2017)

Article Multidisciplinary Sciences

Nascent RNA sequencing reveals distinct features in plant transcription

Jonathan Hetzel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Biochemistry & Molecular Biology

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

Neva C. Durand et al.

CELL SYSTEMS (2016)

Review Plant Sciences

RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants

Marjori A. Matzke et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 66 (2015)

Article Multidisciplinary Sciences

DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

Xuehua Zhong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biotechnology & Applied Microbiology

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Nicolas Servant et al.

GENOME BIOLOGY (2015)

Article Biophysics

DNA Methylation Effects on Tetra-Nucleosome Compaction and Aggregation

Isabel Jimenez-Useche et al.

BIOPHYSICAL JOURNAL (2014)

Article Biochemistry & Molecular Biology

Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases

Xuehua Zhong et al.

Article Multidisciplinary Sciences

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

Lianna M. Johnson et al.

NATURE (2014)

Article Biochemistry & Molecular Biology

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Hume Stroud et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Article Multidisciplinary Sciences

SNF2 chromatin remodeler-family proteins FRG1 and-2 are required for RNA-directed DNA methylation

Martin Groth et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Letter Biochemical Research Methods

Exploring long-range genome interactions using the WashU Epigenome Browser

Xin Zhou et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

Xuehua Zhong et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

Article Multidisciplinary Sciences

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

Israel Ausin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Multidisciplinary Sciences

MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

Guillaume Moissiard et al.

SCIENCE (2012)

Article Biochemical Research Methods

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Identification of genes required for de novo DNA methylation in Arabidopsis

Maxim V. C. Greenberg et al.

EPIGENETICS (2011)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Relationship between nucleosome positioning and DNA methylation

Ramakrishna K. Chodavarapu et al.

NATURE (2010)

Review Genetics & Heredity

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

Julie A. Law et al.

NATURE REVIEWS GENETICS (2010)

Article Biochemical Research Methods

BSMAP: whole genome bisulfite sequence MAPping program

Yuanxin Li et al.

BMC BIOINFORMATICS (2009)

Article Genetics & Heredity

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

Andrzej T. Wierzbicki et al.

NATURE GENETICS (2009)

Article Biochemistry & Molecular Biology

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

Israel Ausin et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al.

GENOME BIOLOGY (2009)

Review Multidisciplinary Sciences

Epigenetic inheritance in plants

Ian R. Henderson et al.

NATURE (2007)

Review Genetics & Heredity

Gardening the genome:: DNA methylation in Arabidopsis thaliana

SWL Chan et al.

NATURE REVIEWS GENETICS (2005)

Article Multidisciplinary Sciences

RNA polymerase IV directs silencing of endogenous DNA

AJ Herr et al.

SCIENCE (2005)

Article Biochemistry & Molecular Biology

Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing

XF Cao et al.

CURRENT BIOLOGY (2002)

Article Multidisciplinary Sciences

Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase

JP Jackson et al.

NATURE (2002)