Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression

Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development

(2019) Kris G. Alavattam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase

(2019) Lucas Patel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

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

(2019) Simon Alberti et al.   CELL

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

(2019) David Trombley McSwiggen et al.   eLife

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

(2019) Mustafa Mir et al.   DEVELOPMENT

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization

(2019) Hisashi Miura et al.   NATURE GENETICS

Quantifying Dynamics in Phase-Separated Condensates Using Fluorescence Recovery after Photobleaching

(2019) Nicole O. Taylor et al.   BIOPHYSICAL JOURNAL

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

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

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

Structural Basis of Heterochromatin Formation by Human HP1

(2018) Shinichi Machida et al.   MOLECULAR CELL

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Physical principles of intracellular organization via active and passive phase transitions

(2018) Joel Berry et al.   REPORTS ON PROGRESS IN PHYSICS

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

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

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

RNA polymerase II clustering through carboxy-terminal domain phase separation

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

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

High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies

(2018) Marie-Odile Baudement et al.   GENOME RESEARCH

A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells

(2018) Doris Berchtold et al.   MOLECULAR CELL

Identifying Nuclear Matrix-Attached DNA Across the Genome

(2017) Jason R. Dobson et al.   JOURNAL OF CELLULAR PHYSIOLOGY

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

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

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

Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress

(2017) Meiyan Jin et al.   Cell Reports

Coexisting Liquid Phases Underlie Nucleolar Subcompartments

(2016) Marina Feric et al.   CELL

Towards an understanding of regulating Cajal body activity by protein modification

(2016) Michael D. Hebert et al.   RNA Biology

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Inverse Size Scaling of the Nucleolus by a Concentration-Dependent Phase Transition

(2015) Stephanie C. Weber et al.   CURRENT BIOLOGY

Nuclear bodies: the emerging biophysics of nucleoplasmic phases

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

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization

(2015) Vuthy Ea et al.   Genes

Liquid-Liquid Phase Separation in Biology

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

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

(2014) A. Grob et al.   GENES & DEVELOPMENT

The Quantitative Nuclear Matrix Proteome as a Biochemical Snapshot of Nuclear Organization

(2014) Rudolf Engelke et al.   JOURNAL OF PROTEOME RESEARCH

Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles

(2014) David Zwicker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Sequence in the Drosophila H3-H4 Promoter Triggers Histone Locus Body Assembly and Biosynthesis of Replication-Coupled Histone mRNAs

(2013) Harmony R. Salzler et al.   DEVELOPMENTAL CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles

(2012) Takao Naganuma et al.   EMBO JOURNAL

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

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

Structure of a Key Intermediate of the SMN Complex Reveals Gemin2's Crucial Function in snRNP Assembly

(2011) Rundong Zhang et al.   CELL

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modulated contact frequencies at gene-rich loci support a statistical helix model for mammalian chromatin organization

(2011) Franck Court et al.   GENOME BIOLOGY

PML Nuclear Bodies

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

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

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

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

Genomic Matrix Attachment Region and Chromosome Conformation Capture Quantitative Real Time PCR Assays Identify Novel Putative Regulatory Elements at the ImprintedDlk1/Gtl2Locus

(2008) Caroline Braem et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

De Novo Formation of a Subnuclear Body

(2008) T. E. Kaiser et al.   SCIENCE