Divide and Rule: Phase Separation in Eukaryotic Genome Functioning

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

(2020) Thomas Cremer et al.   BIOESSAYS

Liquid-Liquid Phase Separation of Histone Proteins in Cells: Role in Chromatin Organization

(2020) Anisha Shakya et al.   BIOPHYSICAL JOURNAL

Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation

(2020) Fabian Erdel et al.   MOLECULAR CELL

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Mechanisms and Functions of Chromosome Compartmentalization

(2020) Erica M. Hildebrand et al.   TRENDS IN BIOCHEMICAL SCIENCES

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

(2020) Preston R. Arnold et al.   Frontiers in Cell and Developmental Biology

Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation

(2020) Lukas Frank et al.   JOURNAL OF MOLECULAR BIOLOGY

Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression

(2020) Yi Lu et al.   NATURE CELL BIOLOGY

ENL initiates multivalent phase separation of the super elongation complex (SEC) in controlling rapid transcriptional activation

(2020) Chenghao Guo et al.   Science Advances

MeCP2 links heterochromatin condensates and neurodevelopmental disease

(2020) Charles H. Li et al.   NATURE

Biomolecular Condensates in the Nucleus

(2020) Benjamin R. Sabari et al.   TRENDS IN BIOCHEMICAL SCIENCES

Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila

(2019) Sergey V. Ulianov et al.   Nature Communications

Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

(2019) Sreejith J. Nair et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Bridging biophysics and neurology: aberrant phase transitions in neurodegenerative disease

(2019) Natalia B. Nedelsky et al.   Nature Reviews Neurology

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

Disordered domains in chromatin-binding proteins

(2019) Matthew Watson et al.   Essays in Biochemistry

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

ATP, Mg2+, Nuclear Phase Separation, and Genome Accessibility

(2019) Roni H.G. Wright et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster

(2019) René M. Marsano et al.   TRENDS IN GENETICS

Disruption of nuclear speckles reduces chromatin interactions in active compartments

(2019) Shibin Hu et al.   Epigenetics & Chromatin

RNA is a critical element for the sizing and the composition of phase-separated RNA–protein condensates

(2019) Marina Garcia-Jove Navarro et al.   Nature Communications

Liquid–Liquid Phase Separation in Disease

(2019) Simon Alberti et al.   Annual Review of Genetics

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation

(2019) Andrew D. Stephens et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2019) Liang Wang et al.   MOLECULAR CELL

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences

(2019) David T. McSwiggen et al.   GENES & DEVELOPMENT

The Significance of the Intrinsically Disordered Regions for the Functions of the bHLH Transcription Factors

(2019) Aneta Tarczewska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Gene expression amplification by nuclear speckle association

(2019) Jiah Kim et al.   JOURNAL OF CELL BIOLOGY

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation

(2019) Xiangru Huo et al.   MOLECULAR CELL

Super-enhancers in transcriptional regulation and genome organization

(2019) Xi Wang et al.   NUCLEIC ACIDS RESEARCH

Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions

(2019) Kyle Xiong et al.   Nature Communications

Impaired cell fate through gain-of-function mutations in a chromatin reader

(2019) Liling Wan et al.   NATURE

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

The Role of RNA in Biological Phase Separations

(2018) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins

(2018) Andrew D. Stephens et al.   MOLECULAR BIOLOGY OF THE CELL

Structural Basis of Heterochromatin Formation by Human HP1

(2018) Shinichi Machida et al.   MOLECULAR CELL

Forces driving the three‐dimensional folding of eukaryotic genomes

(2018) Alvaro Rada‐Iglesias et al.   Molecular Systems Biology

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Paraspeckles: Where Long Noncoding RNA Meets Phase Separation

(2018) Archa H. Fox et al.   TRENDS IN BIOCHEMICAL SCIENCES

Who's In and Who's Out—Compositional Control of Biomolecular Condensates

(2018) Jonathon A. Ditlev et al.   JOURNAL OF MOLECULAR BIOLOGY

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly?

(2018) Aishwarya Gurumurthy et al.   BIOESSAYS

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

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

Defining the Transcriptional Ecosystem

(2018) Maruhen A.D. Silveira et al.   MOLECULAR CELL

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Highly disordered histone H1−DNA model complexes and their condensates

(2018) Abigail L. Turner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membraneless nuclear organelles and the search for phases within phases

(2018) Iain A. Sawyer et al.   Wiley Interdisciplinary Reviews-RNA

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

(2017) Jingyi Fei et al.   JOURNAL OF CELL SCIENCE

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Shaping epigenetic memory via genomic bookmarking

(2017) Davide Michieletto et al.   NUCLEIC ACIDS RESEARCH

Intrinsically Disordered Proteome of Human Membrane-Less Organelles

(2017) April L. Darling et al.   PROTEOMICS

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

(2017) Tyler S Harmon et al.   eLife

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

From single genes to entire genomes: the search for a function of nuclear organization

(2016) Ringo Pueschel et al.   DEVELOPMENT

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Specific genomic cues regulate Cajal body assembly

(2016) Iain A. Sawyer et al.   RNA Biology

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

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

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

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Nuclear bodies: the emerging biophysics of nucleoplasmic phases

(2015) Lian Zhu et al.   CURRENT OPINION IN CELL BIOLOGY

Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

(2015) Fanchi Meng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Pausing of RNA Polymerase II Regulates Mammalian Developmental Potential through Control of Signaling Networks

(2015) Lucy H. Williams et al.   MOLECULAR CELL

Evolution of disorder in Mediator complex and its functional relevance

(2015) Malini Nagulapalli et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose)

(2015) Matthias Altmeyer et al.   Nature Communications

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

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

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

(2012) Tom Sexton et al.   CELL

Higher-order chromatin structure: bridging physics and biology

(2012) Geoffrey Fudenberg et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Contribution of the C-terminal Regions of Promyelocytic Leukemia Protein (PML) Isoforms II and V to PML Nuclear Body Formation

(2012) Yunyun Geng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Super Elongation Complex Family of RNA Polymerase II Elongation Factors: Gene Target Specificity and Transcriptional Output

(2012) Z. Luo et al.   MOLECULAR AND CELLULAR BIOLOGY

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

The super elongation complex (SEC) family in transcriptional control

(2012) Zhuojuan Luo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells

(2012) Saera Hihara et al.   Cell Reports

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

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

Transcription factories in the context of the nuclear and genome organization

(2011) S. V. Razin et al.   NUCLEIC ACIDS RESEARCH

Biogenesis and function of nuclear bodies

(2011) Yuntao S. Mao et al.   TRENDS IN GENETICS

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

PML Nuclear Bodies

(2010) V. Lallemand-Breitenbach et al.   Cold Spring Harbor Perspectives in Biology

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Nuclear Bodies: Random Aggregates of Sticky Proteins or Crucibles of Macromolecular Assembly?

(2009) A. Gregory Matera et al.   DEVELOPMENTAL CELL

Transcription factories: gene expression in unions?

(2009) Heidi Sutherland et al.   NATURE REVIEWS GENETICS

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

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

Transcription factories

(2008) David R.F. Carter et al.   BIOCHEMICAL SOCIETY TRANSACTIONS