On the relations of phase separation and Hi-C maps to epigenetics

H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification

(2019) Dario Nicetto et al.   SCIENCE

Maternal regulation of chromosomal imprinting in animals

(2019) Prim B. Singh et al.   CHROMOSOMA

Role of H3K9me3 heterochromatin in cell identity establishment and maintenance

(2019) Dario Nicetto et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Polymer coil–globule phase transition is a universal folding principle of Drosophila epigenetic domains

(2019) Antony Lesage et al.   Epigenetics & Chromatin

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

SETDB1-dependent heterochromatin stimulates alternative lengthening of telomeres

(2019) Mathilde Gauchier et al.   Science Advances

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2

(2019) Aaron J. Plys et al.   GENES & DEVELOPMENT

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing

(2019) Guido A. Stoll et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism

(2019) Liang Wang et al.   MOLECULAR CELL

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

Function and Regulation of Phase-Separated Biological Condensates

(2018) Xiao-Han Li et al.   BIOCHEMISTRY

The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation

(2018) Adam G. Larson et al.   BIOCHEMISTRY

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Structural Basis of Heterochromatin Formation by Human HP1

(2018) Shinichi Machida et al.   MOLECULAR CELL

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin domains rich in inheritance

(2018) Danny Reinberg et al.   SCIENCE

Entropic effect of macromolecular crowding enhances binding between nucleosome clutches in heterochromatin, but not in euchromatin

(2018) Inrok Oh et al.   Scientific Reports

Heterochromatin: Guardian of the Genome

(2018) Aniek Janssen et al.   Annual Review of Cell and Developmental Biology

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

(2018) Roubina Tatavosian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bottom–up modeling of chromatin segregation due to epigenetic modifications

(2018) Quinn MacPherson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis

(2017) Stefanie A. Baril et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Density imaging of heterochromatin in live cells using orientation-independent-DIC microscopy

(2017) Ryosuke Imai et al.   MOLECULAR BIOLOGY OF THE CELL

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes

(2017) Justin S. Becker et al.   MOLECULAR CELL

Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging

(2017) Tadasu Nozaki et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain

(2017) Yan Jiang et al.   NATURE GENETICS

Ten principles of heterochromatin formation and function

(2017) Robin C. Allshire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Shaping epigenetic memory via genomic bookmarking

(2017) Davide Michieletto et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Molecular Criteria for Defining the Naive Human Pluripotent State

(2016) Thorold W. Theunissen et al.   Cell Stem Cell

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

How to rule the nucleus: divide et impera

(2016) Irina Solovei et al.   CURRENT OPINION IN CELL BIOLOGY

ATRX binds to atypical chromatin domains at the 3′ exons of zinc finger genes to preserve H3K9me3 enrichment

(2016) David Valle-García et al.   Epigenetics

Nucleolar organizer regions: genomic ‘dark matter’ requiring illumination

(2016) Brian McStay   GENES & DEVELOPMENT

Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals

(2016) Prim B Singh   JOURNAL OF BIOSCIENCES

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

(2016) Viviana I. Risca et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

A two-state activation mechanism controls the histone methyltransferase Suv39h1

(2016) Manuel M Müller et al.   Nature Chemical Biology

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The physics of epigenetics

(2016) Ruggero Cortini et al.   REVIEWS OF MODERN PHYSICS

Histone and DNA Modifications as Regulators of Neuronal Development and Function

(2016) Stavros Lomvardas et al.   Cold Spring Harbor Perspectives in Biology

Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin

(2016) Kyoko Hiragami-Hamada et al.   Nature Communications

A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2

(2016) Marti Borkent et al.   Stem Cell Reports

Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

(2015) Bin Xia Yang et al.   CELL

Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

(2015) Kyle P. Eagen et al.   CELL

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

Grabbing the genome by the NADs

(2015) Timothy D. Matheson et al.   CHROMOSOMA

Characterization and dynamics of pericentromere-associated domains in mice

(2015) Patrick J. Wijchers et al.   GENOME RESEARCH

Phosphatidylinositol-4-phosphate 5-Kinase 1α Modulates Ribosomal RNA Gene Silencing through Its Interaction with Histone H3 Lysine 9 Trimethylation and Heterochromatin Protein HP1-α

(2015) Rajarshi Chakrabarti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells

(2015) Simon J. Elsässer et al.   NATURE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The histone chaperone CAF-1 safeguards somatic cell identity

(2015) Sihem Cheloufi et al.   NATURE

RNA transcription modulates phase transition-driven nuclear body assembly

(2015) Joel Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The histone chaperone DAXX maintains the structural organization of heterochromatin domains

(2015) Lindsy M. Rapkin et al.   Epigenetics & Chromatin

Constitutive heterochromatin formation and transcription in mammals

(2015) Nehmé Saksouk et al.   Epigenetics & Chromatin

ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes

(2015) Hsiao P.J. Voon et al.   Cell Reports

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

(2015) Ruslan Strogantsev et al.   GENOME BIOLOGY

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

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

(2014) Suhas S.P. Rao et al.   CELL

Embryonic Development following Somatic Cell Nuclear Transfer Impeded by Persisting Histone Methylation

(2014) Shogo Matoba et al.   CELL

Chromosome boundary elements and regulation of heterochromatin spreading

(2014) Jiyong Wang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The developmental hourglass model: a predictor of the basic body plan?

(2014) N. Irie et al.   DEVELOPMENT

Telomere position effect: regulation of gene expression with progressive telomere shortening over long distances

(2014) Jérôme D. Robin et al.   GENES & DEVELOPMENT

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos

(2014) D. M. Messerschmidt et al.   GENES & DEVELOPMENT

Human Heterochromatin Protein 1α Promotes Nucleosome Associations That Drive Chromatin Condensation

(2014) Abdelhamid M. Azzaz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quiescence-Induced LncRNAs Trigger H4K20 Trimethylation and Transcriptional Silencing

(2014) Holger Bierhoff et al.   MOLECULAR CELL

Specificity, propagation, and memory of pericentric heterochromatin

(2014) K. Muller-Ott et al.   Molecular Systems Biology

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Nuclear compartmentalization of odorant receptor genes

(2014) L. M. Armelin-Correa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1

(2014) D. Leung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterochromatin-Mediated Gene Silencing Facilitates the Diversification of Olfactory Neurons

(2014) David B. Lyons et al.   Cell Reports

LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation

(2013) Irina Solovei et al.   CELL

De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET

(2013) H. M. Rowe et al.   DEVELOPMENT

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

(2013) Rupa Sridharan et al.   NATURE CELL BIOLOGY

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

(2013) Emily V. Chambers et al.   PLoS Computational Biology

Aqueous Phase Separation as a Possible Route to Compartmentalization of Biological Molecules

(2012) Christine D. Keating   ACCOUNTS OF CHEMICAL RESEARCH

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

(2012) E. Josephine Clowney et al.   CELL

Self-assembly of block copolymers

(2012) Yiyong Mai et al.   CHEMICAL SOCIETY REVIEWS

Characterization of Chromoshadow Domain-mediated Binding of Heterochromatin Protein 1α (HP1α) to Histone H3

(2012) Alexandria N. Richart et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An epigenetic silencing pathway controlling T helper 2 cell lineage commitment

(2012) Rhys S. Allan et al.   NATURE

H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs

(2012) Jiekai Chen et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

(2012) Hisato Kobayashi et al.   PLoS Genetics

Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins

(2012) Gary LeRoy et al.   GENOME BIOLOGY

Loss of Heterochromatin Protein 1 Gamma Reduces the Number of Primordial Germ Cells via Impaired Cell Cycle Progression in Mice1

(2011) Kanae Abe et al.   BIOLOGY OF REPRODUCTION

An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

(2011) Angeliki Magklara et al.   CELL

Keeping chromatin quiet

(2011) Jacqueline E. Mermoud et al.   CELL CYCLE

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

HP1  links histone methylation marks to meiotic synapsis in mice

(2011) Y. Takada et al.   DEVELOPMENT

Combinatorial Readout of Dual Histone Modifications by Paired Chromatin-associated Modules

(2011) Zhanxin Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Zinc Finger Protein ZFP57 Requires Its Co-factor to Recruit DNA Methyltransferases and Maintains DNA Methylation Imprint in Embryonic Stem Cells via Its Transcriptional Repression Domain

(2011) Xiaopan Zuo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

KAP1 Protein: An Enigmatic Master Regulator of the Genome

(2011) Sushma Iyengar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Oligomerization and Binding of the Dnmt3a DNA Methyltransferase to Parallel DNA Molecules

(2011) Renata Z. Jurkowska et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Maintenance of Silent Chromatin through Replication Requires SWI/SNF-like Chromatin Remodeler SMARCAD1

(2011) Samuel P. Rowbotham et al.   MOLECULAR CELL

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin

(2011) Sebastian Eustermann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes

(2011) C. P. Brangwynne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mammalian Su(var) Genes in Chromatin Control

(2010) Barna D. Fodor et al.   Annual Review of Cell and Developmental Biology

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats

(2010) Claudio Guetg et al.   EMBO JOURNAL

The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3

(2010) P. Drane et al.   GENES & DEVELOPMENT

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

ATRX interacts with H3.3 in maintaining telomere structural integrity in pluripotent embryonic stem cells

(2010) L. H. Wong et al.   GENOME RESEARCH

ZNF274 Recruits the Histone Methyltransferase SETDB1 to the 3′ Ends of ZNF Genes

(2010) Seth Frietze et al.   PLoS One

HP1 proteins—What is the essential interaction?

(2010) P. B. Singh   RUSSIAN JOURNAL OF GENETICS

HP1γ function is required for male germ cell survival and spermatogenesis

(2010) Jeremy P Brown et al.   Epigenetics & Chromatin

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

(2010) Anna C. Groner et al.   PLoS Genetics

Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution

(2009) Irina Solovei et al.   CELL

Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin

(2009) Aurélien Bancaud et al.   EMBO JOURNAL

The HP1α–CAF1–SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin

(2009) Alejandra Loyola et al.   EMBO REPORTS

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

The secret message of heterochromatin: new insights into the mechanisms and function of centromeric and pericentric repeat sequence transcription

(2009) Angeline Eymery et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Loss of Human Ribosomal Gene CpG Methylation Enhances Cryptic RNA Polymerase II Transcription and Disrupts Ribosomal RNA Processing

(2009) Thérèse Gagnon-Kugler et al.   MOLECULAR CELL

Spatially confined folding of chromatin in the interphase nucleus

(2009) J. Mateos-Langerak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) E. Lieberman-Aiden et al.   SCIENCE

The essential function of HP1β: a case of the tail wagging the dog?

(2009) Mustafa Billur et al.   TRENDS IN BIOCHEMICAL SCIENCES

Interaction of HP1 and Brg1/Brm with the Globular Domain of Histone H3 Is Required for HP1-Mediated Repression

(2009) Marc Lavigne et al.   PLoS Genetics

Association of ATRX with pericentric heterochromatin and the Y chromosome of neonatal mouse spermatogonia

(2008) Claudia Baumann et al.   BMC MOLECULAR BIOLOGY

Epigenetic Control of rDNA Loci in Response to Intracellular Energy Status

(2008) Akiko Murayama et al.   CELL

Micromechanical studies of mitotic chromosomes

(2008) John F. Marko   CHROMOSOME RESEARCH

PR-SET7 and SUV4-20H regulate H4 lysine-20 methylation at imprinting control regions in the mouse

(2008) Maëlle Pannetier et al.   EMBO REPORTS

HP1-β is required for development of the cerebral neocortex and neuromuscular junctions

(2008) Rebecca Aucott et al.   JOURNAL OF CELL BIOLOGY

The PHD Domain of Np95 (mUHRF1) Is Involved in Large-Scale Reorganization of Pericentromeric Heterochromatin

(2008) Roberto Papait et al.   MOLECULAR BIOLOGY OF THE CELL