Nuclear compartmentalization as a mechanism of quantitative control of gene expression

Structure of a transcribing RNA polymerase II–U1 snRNP complex

(2021) Suyang Zhang et al.   SCIENCE

Speed–Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites

(2021) Tamar Jana et al.   TRENDS IN GENETICS

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

p53 mediates target gene association with nuclear speckles for amplified RNA expression

(2021) Katherine A. Alexander et al.   MOLECULAR CELL

Understanding 3D genome organization by multidisciplinary methods

(2021) Ivana Jerkovic´ et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rett syndrome-causing mutations compromise MeCP2-mediated liquid–liquid phase separation of chromatin

(2020) Liang Wang et al.   CELL RESEARCH

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

(2020) Fabian Erdel et al.   MOLECULAR CELL

SPEN integrates transcriptional and epigenetic control of X-inactivation

(2020) François Dossin et al.   NATURE

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

(2020) Yi Lu et al.   NATURE CELL BIOLOGY

Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation

(2020) Mackenzie Strehle et al.   CURRENT OPINION IN CELL BIOLOGY

Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins

(2020) Joseph Dopie et al.   JOURNAL OF CELL BIOLOGY

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

MeCP2 links heterochromatin condensates and neurodevelopmental disease

(2020) Charles H. Li et al.   NATURE

Methods to Study Phase-Separated Condensates and the Underlying Molecular Interactions

(2020) Laura R. Ganser et al.   TRENDS IN BIOCHEMICAL SCIENCES

Biomolecular Condensates in the Nucleus

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

Rett mutations attenuate phase separation of MeCP2

(2020) Chunyan Fan et al.   Cell Discovery

A protein assembly mediates Xist localization and gene silencing

(2020) Amy Pandya-Jones et al.   NATURE

The nucleolus as a multiphase liquid condensate

(2020) Denis L. J. Lafontaine et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA nucleation by MSL2 induces selective X chromosome compartmentalization

(2020) Claudia Isabelle Keller Valsecchi et al.   NATURE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Constitutive splicing and economies of scale in gene expression

(2019) Fangyuan Ding et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Phase separation drives X-chromosome inactivation: a hypothesis

(2019) Andrea Cerase et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

(2019) David Trombley McSwiggen et al.   eLife

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Chromatin folding and nuclear architecture: PRC1 function in 3D

(2019) Robert S Illingworth   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

LADL: light-activated dynamic looping for endogenous gene expression control

(2019) Ji Hun Kim et al.   NATURE METHODS

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

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

(2019) Liang Wang et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Xist RNA in action: Past, present, and future

(2019) Agnese Loda et al.   PLoS Genetics

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

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

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

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs

(2019) William A. Flavahan et al.   NATURE

Resolving noise–control conflict by gene duplication

(2019) Michal Chapal et al.   PLOS BIOLOGY

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

(2018) Sofia A. Quinodoz et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Single-molecule photobleaching: Instrumentation and applications

(2018) Simli Dey et al.   JOURNAL OF BIOSCIENCES

Introduction to fluorescence correlation Spectroscopy—Brief and simple

(2018) Elliot L. Elson   METHODS

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

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

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

(2018) Yu Chen et al.   JOURNAL OF CELL 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

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang 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

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda 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

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

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

Birth and Death of Histone mRNAs

(2017) William F. Marzluff et al.   TRENDS IN GENETICS

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

New Xist -Interacting Proteins in X-Chromosome Inactivation

(2016) Hegias Mira-Bontenbal et al.   CURRENT BIOLOGY

Nucleation by rRNA Dictates the Precision of Nucleolus Assembly

(2016) Hanieh Falahati et al.   CURRENT BIOLOGY

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

(2016) Zhengjian Zhang et al.   GENES & DEVELOPMENT

Design of a hyperstable 60-subunit protein icosahedron

(2016) Yang Hsia et al.   NATURE

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

Protein stability: a crystallographer's perspective

(2016) Marc C. Deller et al.   Acta Crystallographica Section F-Structural Biology Communications

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Polymer physics of intracellular phase transitions

(2015) Clifford P. Brangwynne et al.   Nature Physics

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

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

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

(2015) Matthias Altmeyer et al.   Nature Communications

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing

(2015) Benoit Moindrot et al.   Cell Reports

Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells

(2015) Asun Monfort et al.   Cell Reports

Liquid-Liquid Phase Separation in Biology

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

Super-resolution Microscopy Approaches for Live Cell Imaging

(2014) Antoine G. Godin et al.   BIOPHYSICAL JOURNAL

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Nucleolus and nuclear periphery: Velcro for heterochromatin

(2014) Jan Padeken et al.   CURRENT OPINION IN CELL BIOLOGY

The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies

(2014) Martin Machyna et al.   MOLECULAR CELL

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

RNA Polymerase II CTD Modifications: How Many Tales From a Single Tail

(2013) Giuliana Napolitano et al.   JOURNAL OF CELLULAR PHYSIOLOGY

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   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

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion

(2012) Cyrille Girard et al.   Nature Communications

A view of nuclear Polycomb bodies

(2011) Vincenzo Pirrotta et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

RNA seeds nuclear bodies

(2011) Maria Carmo-Fonseca et al.   NATURE CELL BIOLOGY

Nucleation of nuclear bodies by RNA

(2011) Sergey P. Shevtsov et al.   NATURE CELL BIOLOGY

Kcnq1ot1: A chromatin regulatory RNA

(2011) Chandrasekhar Kanduri   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Pre-mRNA splicing: where and when in the nucleus

(2011) Joonhee Han et al.   TRENDS IN CELL BIOLOGY

The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA

(2011) Nicholas J. Watkins et al.   Wiley Interdisciplinary Reviews-RNA

Application of protein engineering to enhance crystallizability and improve crystal properties

(2010) Zygmunt S. Derewenda   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells

(2010) Bo Huang et al.   CELL

Recruitment Timing and Dynamics of Transcription Factors at the Hsp70 Loci in Living Cells

(2010) Katie L. Zobeck et al.   MOLECULAR CELL

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

The Cajal Body and Histone Locus Body

(2010) Z. Nizami et al.   Cold Spring Harbor Perspectives in Biology

Biogenesis of Nuclear Bodies

(2010) M. Dundr et al.   Cold Spring Harbor Perspectives in Biology

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

Emerging similarities in epigenetic gene silencing by long noncoding RNAs

(2009) Takashi Nagano et al.   MAMMALIAN GENOME

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

Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence

(2008) R. Ileng Kumaran et al.   JOURNAL OF CELL BIOLOGY

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics