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Shaping Epigenetic Memory via Genomic Bookmarking: Supplementary Information

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1 of the 82 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-04): 10.7554/elife.12248 (notice 2018-04-12).

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What this work says

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

inferredcites →https://doi.org/10.1002/bies.201700053openalex-snapshot

How Communication Between Nucleosomes Enables Spreading and Epigenetic Memory of Histone Modifications

inferredcites →https://doi.org/10.1007/s10577-010-9177-0openalex-snapshot

The fractal globule as a model of chromatin architecture in the cell

inferredcites →https://doi.org/10.1016/b978-0-12-407677-8.00003-8openalex-snapshot

Polycomb Group Response Elements in Drosophila and Vertebrates

inferredcites →https://doi.org/10.1016/j.bpj.2010.01.054openalex-snapshot

Looping Probabilities in Model Interphase Chromosomes

inferredcites →https://doi.org/10.1016/j.bpj.2017.01.025openalex-snapshot

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains

inferredcites →https://doi.org/10.1016/j.cell.2007.02.053openalex-snapshot

Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification

inferredcites →https://doi.org/10.1016/j.cell.2010.09.009openalex-snapshot

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

inferredcites →https://doi.org/10.1016/j.cell.2012.01.010openalex-snapshot

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

inferredcites →https://doi.org/10.1016/j.cell.2012.03.052openalex-snapshot

Dynamics and Memory of Heterochromatin in Living Cells

inferredcites →https://doi.org/10.1016/j.cell.2012.06.038openalex-snapshot

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

inferredcites →https://doi.org/10.1016/j.cell.2014.02.045openalex-snapshot

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

inferredcites →https://doi.org/10.1016/j.cell.2014.05.050openalex-snapshot

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

inferredcites →https://doi.org/10.1016/j.cell.2017.05.029openalex-snapshot

SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs

inferredcites →https://doi.org/10.1016/j.celrep.2012.03.012openalex-snapshot

Epigenetically Heritable Alteration of Fly Development in Response to Toxic Challenge

inferredcites →https://doi.org/10.1016/j.celrep.2012.12.020openalex-snapshot

Global Changes in the Mammary Epigenome Are Induced by Hormonal Cues and Coordinated by Ezh2

inferredcites →https://doi.org/10.1016/j.celrep.2014.08.072openalex-snapshot

Cooperativity, Specificity, and Evolutionary Stability of Polycomb Targeting in Drosophila

inferredcites →https://doi.org/10.1016/j.celrep.2016.04.085openalex-snapshot

Formation of Chromosomal Domains by Loop Extrusion

inferredcites →https://doi.org/10.1016/j.celrep.2016.08.096openalex-snapshot

A High-Density Map for Navigating the Human Polycomb Complexome

inferredcites →https://doi.org/10.1016/j.celrep.2016.11.032openalex-snapshot

Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells

inferredcites →https://doi.org/10.1016/j.cels.2017.02.013openalex-snapshot

Slow Chromatin Dynamics Allow Polycomb Target Genes to Filter Fluctuations in Transcription Factor Activity

inferredcites →https://doi.org/10.1016/j.jmb.2011.10.027openalex-snapshot

Barriers and Silencers: A Theoretical Toolkit for Control and Containment of Nucleosome-Based Epigenetic States

inferredcites →https://doi.org/10.1016/j.jmb.2016.12.009openalex-snapshot

The Epigenetic Paradox of Pluripotent ES Cells

inferredcites →https://doi.org/10.1016/j.jtbi.2013.07.012openalex-snapshot

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

inferredcites →https://doi.org/10.1016/j.tibs.2005.09.004openalex-snapshot

Gene bookmarking: keeping the pages open

inferredcites →https://doi.org/10.1016/j.tibs.2010.05.006openalex-snapshot

Fast signals and slow marks: the dynamics of histone modifications

inferredcites →https://doi.org/10.1016/j.tig.2015.07.001openalex-snapshot

Why the activity of a gene depends on its neighbors

inferredcites →https://doi.org/10.1016/s0074-7696(04)42007-5openalex-snapshot

Chromatin Organization in the Mammalian Nucleus

inferredcites →https://doi.org/10.1038/150563a0openalex-snapshot

CANALIZATION OF DEVELOPMENT AND THE INHERITANCE OF ACQUIRED CHARACTERS

inferredcites →https://doi.org/10.1038/47412openalex-snapshot

The language of covalent histone modifications

inferredcites →https://doi.org/10.1038/nature09725openalex-snapshot

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

inferredcites →https://doi.org/10.1038/nature10241openalex-snapshot

A Polycomb-based switch underlying quantitative epigenetic memory

inferredcites →https://doi.org/10.1038/nature11082openalex-snapshot

Topological domains in mammalian genomes identified by analysis of chromatin interactions

inferredcites →https://doi.org/10.1038/nature14222openalex-snapshot

Chromatin architecture reorganization during stem cell differentiation

inferredcites →https://doi.org/10.1038/ncb1637openalex-snapshot

Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex

inferredcites →https://doi.org/10.1038/ncb1674openalex-snapshot

Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription

inferredcites →https://doi.org/10.1038/ncb3418openalex-snapshot

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

inferredcites →https://doi.org/10.1038/ncomms11518openalex-snapshot

Nucleation and spreading of a heterochromatic domain in fission yeast

inferredcites →https://doi.org/10.1038/ng.3848openalex-snapshot

Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila

inferredcites →https://doi.org/10.1038/nrg1920openalex-snapshot

Spreading of silent chromatin: inaction at a distance

inferredcites →https://doi.org/10.1038/nrm2640openalex-snapshot

Epigenetic inheritance during the cell cycle

inferredcites →https://doi.org/10.1038/nsmb.2470openalex-snapshot

Regulation of nucleosome dynamics by histone modifications

inferredcites →https://doi.org/10.1038/nsmb.2474openalex-snapshot

Functional implications of genome topology

inferredcites →https://doi.org/10.1038/s41598-017-13916-wopenalex-snapshot

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

inferredcites →https://doi.org/10.1038/sj.emboj.7600516openalex-snapshot

Histone modifications defining active genes persist after transcriptional and mitotic inactivation

inferredcites →https://doi.org/10.1042/bse0480107openalex-snapshot

Epigenetic dynamics across the cell cycle

inferredcites →https://doi.org/10.1042/bss0730059openalex-snapshot

The relationship between higher-order chromatin structure and transcription

inferredcites →https://doi.org/10.1073/pnas.1204799109openalex-snapshot

Complexity of chromatin folding is captured by the strings and binders switch model

inferredcites →https://doi.org/10.1073/pnas.1302950110openalex-snapshot

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

inferredcites →https://doi.org/10.1073/pnas.1518552112openalex-snapshot

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

inferredcites →https://doi.org/10.1073/pnas.1605862113openalex-snapshot

Generalized nucleation and looping model for epigenetic memory of histone modifications

inferredcites →https://doi.org/10.1073/pnas.1613607113openalex-snapshot

Transferable model for chromosome architecture

inferredcites →https://doi.org/10.1080/19491034.2016.1239684openalex-snapshot

Simulating topological domains in human chromosomes with a fitting-free model

inferredcites →https://doi.org/10.1088/1478-3975/7/2/026010openalex-snapshot

Theory for the stability and regulation of epigenetic landscapes

inferredcites →https://doi.org/10.1093/emboj/21.5.1121openalex-snapshot

Central role of Drosophila SU(VAR)3–9 in histone H3‐K9 methylation and heterochromatic gene silencing

inferredcites →https://doi.org/10.1093/nar/gkp518openalex-snapshot

Establishment of Histone Modifications after Chromatin Assembly

inferredcites →https://doi.org/10.1093/nar/gkt1324openalex-snapshot

Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases

inferredcites →https://doi.org/10.1093/nar/gkw135openalex-snapshot

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

inferredcites →https://doi.org/10.1101/gad.234591.113openalex-snapshot

Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division

inferredcites →https://doi.org/10.1101/gad.256354.114openalex-snapshot

Two distinct modes for propagation of histone PTMs across the cell cycle

inferredcites →https://doi.org/10.1101/gad.289256.116openalex-snapshot

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

inferredcites →https://doi.org/10.1101/gr.133751.111openalex-snapshot

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

inferredcites →https://doi.org/10.1111/nyas.12262openalex-snapshot

Establishing epigenetic domains via chromatin‐bound histone modifiers

inferredcites →https://doi.org/10.1126/sciadv.1701143openalex-snapshot

Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory

inferredcites →https://doi.org/10.1126/science.1063127openalex-snapshot

Translating the Histone Code

inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

inferredcites →https://doi.org/10.1126/science.1240104openalex-snapshot

Nuclear Lamin-A Scales with Tissue Stiffness and Enhances Matrix-Directed Differentiation

inferredcites →https://doi.org/10.1126/science.aai8236openalex-snapshot

Causal role for inheritance of H3K27me3 in maintaining the OFF state of a Drosophila HOX gene

inferredcites →https://doi.org/10.1126/science.aai8266openalex-snapshot

Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA

inferredcites →https://doi.org/10.1186/1756-8935-6-6openalex-snapshot

Mitotic bookmarking by transcription factors

inferredcites →https://doi.org/10.1186/1756-8935-7-30openalex-snapshot

Mechanistic stochastic model of histone modification pattern formation

inferredcites →https://doi.org/10.1186/s13059-015-0802-2openalex-snapshot

A transient ischemic environment induces reversible compaction of chromatin

inferredcites →https://doi.org/10.1242/dev.091439openalex-snapshot

Histone variants in pluripotency and disease

inferredcites →https://doi.org/10.1371/journal.pcbi.1000153openalex-snapshot

Structure and Dynamics of Interphase Chromosomes

inferredcites →https://doi.org/10.1371/journal.pgen.1002465openalex-snapshot

Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion

inferredcites →https://doi.org/10.1371/journal.pgen.1003135openalex-snapshot

A Polycomb Group Protein Is Retained at Specific Sites on Chromatin in Mitosis

inferredcites →https://doi.org/10.1371/journal.pgen.1005944openalex-snapshot

Glucocerebrosidase Deficiency in Drosophila Results in α-Synuclein-Independent Protein Aggregation and Neurodegeneration

inferredcites →https://doi.org/10.15252/embr.201744292openalex-snapshot

Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation

inferredcites →https://doi.org/10.1530/joe-14-0141openalex-snapshot

Clocks for all seasons: unwinding the roles and mechanisms of circadian and interval timers in the hypothalamus and pituitary

inferredcites →https://doi.org/10.48550/arxiv.1606.04653openalex-snapshot

A Polymer Model with Epigenetic Recolouring Reveals a Pathway for the de novo Establishment and 3D Organisation of Chromatin Domains

inferredcites →https://doi.org/10.7554/elife.06633openalex-snapshot

Ventromedial hypothalamic neurons control a defensive emotion state

inferredcites →https://doi.org/10.7554/elife.12248openalex-snapshot

RETRACTED: A mathematical model explains saturating axon guidance responses to molecular gradients

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.70675/0b1d39b2za3d7z4b26zb4b0zaafa77d5068aopenalex-snapshot

Epigenetic characterization of cellular pliancy in breast cancer

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