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DNA polymerase epsilon is a central coordinator of heterochromatin structure and function in Arabidopsis

https://doi.org/10.1101/2020.05.26.117556

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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00412-015-0545-6openalex-snapshot

Linking replication stress with heterochromatin formation

inferredcites →https://doi.org/10.1007/s10577-005-1022-5openalex-snapshot

Composition and formation of heterochromatin in Arabidopsis thaliana

inferredcites →https://doi.org/10.1016/j.bbagrm.2011.04.001openalex-snapshot

A “mille-feuille” of silencing: Epigenetic control of transposable elements

inferredcites →https://doi.org/10.1016/j.cell.2006.08.003openalex-snapshot

Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis

inferredcites →https://doi.org/10.1016/j.cell.2012.07.034openalex-snapshot

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

inferredcites →https://doi.org/10.1016/j.cell.2012.10.054openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2013.02.033openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2014.06.006openalex-snapshot

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

inferredcites →https://doi.org/10.1016/j.cub.2005.09.013openalex-snapshot

Mutations in a Conserved Replication Protein Suppress Transcriptional Gene Silencing in a DNA- Methylation-Independent Manner in Arabidopsis

inferredcites →https://doi.org/10.1016/j.cub.2005.09.044openalex-snapshot

Arabidopsis RPA2: A Genetic Link among Transcriptional Gene Silencing, DNA Repair, and DNA Replication

inferredcites →https://doi.org/10.1016/j.devcel.2018.05.023openalex-snapshot

Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression

inferredcites →https://doi.org/10.1016/j.molcel.2010.01.033openalex-snapshot

Replication Stress Interferes with Histone Recycling and Predeposition Marking of New Histones

inferredcites →https://doi.org/10.1016/j.molcel.2019.10.011openalex-snapshot

DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts

inferredcites →https://doi.org/10.1016/s0092-8674(01)00197-0openalex-snapshot

FASCIATA Genes for Chromatin Assembly Factor-1 in Arabidopsis Maintain the Cellular Organization of Apical Meristems

inferredcites →https://doi.org/10.1016/s0960-9822(00)00862-9openalex-snapshot

DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis

inferredcites →https://doi.org/10.1038/emboj.2011.103openalex-snapshot

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

inferredcites →https://doi.org/10.1038/nature02651openalex-snapshot

Role of transposable elements in heterochromatin and epigenetic control

inferredcites →https://doi.org/10.1038/nature09290openalex-snapshot

Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

inferredcites →https://doi.org/10.1038/ncomms15122openalex-snapshot

Arabidopsis proteins with a transposon-related domain act in gene silencing

inferredcites →https://doi.org/10.1038/nmeth0305-213openalex-snapshot

Profiling histone modification patterns in plants using genomic tiling microarrays

inferredcites →https://doi.org/10.1038/nprot.2012.101openalex-snapshot

Identifying ChIP-seq enrichment using MACS

inferredcites →https://doi.org/10.1038/nrc2523openalex-snapshot

γH2AX and cancer

inferredcites →https://doi.org/10.1038/nrg.2017.46openalex-snapshot

The impact of replication stress on replication dynamics and DNA damage in vertebrate cells

inferredcites →https://doi.org/10.1038/nrg3961openalex-snapshot

R loops: new modulators of genome dynamics and function

inferredcites →https://doi.org/10.1038/nrm2450openalex-snapshot

ATR: an essential regulator of genome integrity

inferredcites →https://doi.org/10.1038/nrm2861openalex-snapshot

Histone variants — ancient wrap artists of the epigenome

inferredcites →https://doi.org/10.1038/nrm2868openalex-snapshot

MicroRNA control of signal transduction

inferredcites →https://doi.org/10.1038/nrm4043openalex-snapshot

DNA methylation pathways and their crosstalk with histone methylation

inferredcites →https://doi.org/10.1038/nsmb.1611openalex-snapshot

ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing

inferredcites →https://doi.org/10.1038/nsmb.2735openalex-snapshot

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

inferredcites →https://doi.org/10.1073/pnas.1203145109openalex-snapshot

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

inferredcites →https://doi.org/10.1073/pnas.1507165112openalex-snapshot

Formation of interference-sensitive meiotic cross-overs requires sufficient DNA leading-strand elongation

inferredcites →https://doi.org/10.1073/pnas.1614837114openalex-snapshot

Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

inferredcites →https://doi.org/10.1073/pnas.1619774114openalex-snapshot

Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage

inferredcites →https://doi.org/10.1074/jbc.m513426200openalex-snapshot

Functional Genomic Analysis of CAF-1 Mutants in Arabidopsis thaliana

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

inferredcites →https://doi.org/10.1093/emboj/cdf657openalex-snapshot

DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis

inferredcites →https://doi.org/10.1093/nar/gku365openalex-snapshot

deepTools: a flexible platform for exploring deep-sequencing data

inferredcites →https://doi.org/10.1093/nar/gkw156openalex-snapshot

Arabidopsis DNA polymerase ϵ recruits components of Polycomb repressor complex to mediate epigenetic gene silencing

inferredcites →https://doi.org/10.1093/nar/gky1038openalex-snapshot

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

inferredcites →https://doi.org/10.1093/nar/gky540openalex-snapshot

Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility

inferredcites →https://doi.org/10.1101/gad.295404openalex-snapshot

BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis

inferredcites →https://doi.org/10.1104/pp.113.216796openalex-snapshot

The ATM-Dependent DNA Damage Response Acts as an Upstream Trigger for Compensation in thefas1Mutation during Arabidopsis Leaf Development

inferredcites →https://doi.org/10.1104/pp.15.01976openalex-snapshot

The second subunit of DNA-polymerase delta is required for genomic stability and epigenetic regulation

inferredcites →https://doi.org/10.1104/pp.17.00031openalex-snapshot

Function of the Plant DNA Polymerase Epsilon in Replicative Stress Sensing, a Genetic Analysis

inferredcites →https://doi.org/10.1105/tpc.105.036889openalex-snapshot

Interactions between the Cell Cycle and Embryonic Patterning in Arabidopsis Uncovered by a Mutation in DNA Polymerase ε

inferredcites →https://doi.org/10.1105/tpc.107.054361openalex-snapshot

MIDGETUnravels Functions of theArabidopsisTopoisomerase VI Complex in DNA Endoreduplication, Chromatin Condensation, and Transcriptional Silencing

inferredcites →https://doi.org/10.1105/tpc.108.061549openalex-snapshot

Epigenetic Regulation, Somatic Homologous Recombination, and Abscisic Acid Signaling Are Influenced by DNA Polymerase ϵ Mutation inArabidopsis

inferredcites →https://doi.org/10.1105/tpc.110.076349openalex-snapshot

DNA Replication Factor C1 Mediates Genomic Stability and Transcriptional Gene Silencing inArabidopsis

inferredcites →https://doi.org/10.1105/tpc.15.01003openalex-snapshot

Histone H3 Dynamics Reveal Domains with Distinct Proliferation Potential in the Arabidopsis Root

inferredcites →https://doi.org/10.1105/tpc.16.00474openalex-snapshot

DNA DAMAGE BINDING PROTEIN2 Shapes the DNA Methylation Landscape

inferredcites →https://doi.org/10.1111/j.1365-313x.2006.02799.xopenalex-snapshot

Two cell‐cycle regulated SET‐domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis

inferredcites →https://doi.org/10.1111/j.1365-313x.2009.04026.xopenalex-snapshot

Mutation in the catalytic subunit of DNA polymerase α influences transcriptional gene silencing and homologous recombination in Arabidopsis

inferredcites →https://doi.org/10.1111/j.1365-313x.2009.04093.xopenalex-snapshot

EARLY IN SHORT DAYS 7(ESD7) encodes the catalytic subunit of DNA polymerase epsilon and is required for flowering repression through a mechanism involving epigenetic gene silencing

inferredcites →https://doi.org/10.1111/j.1365-313x.2010.04331.xopenalex-snapshot

Xrcc1-dependent and Ku-dependent DNA double-strand break repair kinetics in Arabidopsis plants

inferredcites →https://doi.org/10.1111/nph.15082openalex-snapshot

Transgenerational phenotype aggravation in CAF ‐1 mutants reveals parent‐of‐origin specific epigenetic inheritance

inferredcites →https://doi.org/10.1111/nph.15248openalex-snapshot

Replication‐coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development

inferredcites →https://doi.org/10.1111/tpj.12215openalex-snapshot

Identification of MAIN, a factor involved in genome stability in the meristems of Arabidopsis thaliana

inferredcites →https://doi.org/10.1111/tpj.12455openalex-snapshot

MAIN ‐ LIKE 1 is a crucial factor for correct cell division and differentiation in A rabidopsis thaliana

inferredcites →https://doi.org/10.1111/tpj.13224openalex-snapshot

Requirement for flap endonuclease 1 ( FEN 1) to maintain genomic stability and transcriptional gene silencing in Arabidopsis

inferredcites →https://doi.org/10.1146/annurev-biochem-061516-044709openalex-snapshot

Eukaryotic DNA Replication Fork

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-017-1221-3openalex-snapshot

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

inferredcites →https://doi.org/10.1186/s13059-017-1246-7openalex-snapshot

The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility

inferredcites →https://doi.org/10.1242/dev.02599openalex-snapshot

Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development

inferredcites →https://doi.org/10.1242/dev.084624openalex-snapshot

The catalytic subunit ofArabidopsisDNA polymerase α ensures stable maintenance of histone modification

inferredcites →https://doi.org/10.1371/journal.pgen.1001175openalex-snapshot

Stress-Induced Activation of Heterochromatic Transcription

inferredcites →https://doi.org/10.1371/journal.pgen.1002658openalex-snapshot

Dynamic Deposition of Histone Variant H3.3 Accompanies Developmental Remodeling of the Arabidopsis Transcriptome

inferredcites →https://doi.org/10.1371/journal.pgen.1002808openalex-snapshot

DNA Methyltransferases Are Required to Induce Heterochromatic Re-Replication in Arabidopsis

inferredcites →https://doi.org/10.1371/journal.pgen.1004975openalex-snapshot

The Arabidopsis DNA Polymerase δ Has a Role in the Deposition of Transcriptionally Active Epigenetic Marks, Development and Flowering

inferredcites →https://doi.org/10.1371/journal.pgen.1006092openalex-snapshot

Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana

inferredcites →https://doi.org/10.1371/journal.pgen.1006526openalex-snapshot

DNA Methylation Signatures of the Plant Chromomethyltransferases

inferredcites →https://doi.org/10.1371/journal.pone.0002221openalex-snapshot

A DNA Polymerase α Accessory Protein, Mcl1, Is Required for Propagation of Centromere Structures in Fission Yeast

inferredcites →https://doi.org/10.1371/journal.pone.0003156openalex-snapshot

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

inferredcites →https://doi.org/10.1371/journal.pone.0129137openalex-snapshot

The Cytosolic Iron-Sulfur Cluster Assembly Protein MMS19 Regulates Transcriptional Gene Silencing, DNA Repair, and Flowering Time in Arabidopsis

inferredcites →https://doi.org/10.1534/g3.117.300341openalex-snapshot

Dependency of Heterochromatin Domains on Replication Factors

inferredcites →https://doi.org/10.26508/lsa.201800197openalex-snapshot

A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing

inferredcites →https://doi.org/10.32614/cran.package.nsm3openalex-snapshot

NSM3: Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition

inferredcites →https://doi.org/10.3390/genes7110099openalex-snapshot

The Cell Killing Mechanisms of Hydroxyurea

inferredcites →https://doi.org/10.3390/genes8020074openalex-snapshot

The Intra-S Checkpoint Responses to DNA Damage

inferredcites →https://doi.org/10.3390/v9030057openalex-snapshot

Cross-Regulation between Transposable Elements and Host DNA Replication

inferredcites →https://doi.org/10.7554/elife.30674openalex-snapshot

DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes

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