DNA-binding, multivalent interactions and phase separation in transcriptional activation

Emerging mechanisms and dynamics of three-dimensional genome organisation at zygotic genome activation

(2022) Elizabeth Ing-Simmons et al.   CURRENT OPINION IN CELL BIOLOGY

BRD4-directed super-enhancer organization of transcription repression programs links to chemotherapeutic efficacy in breast cancer

(2022) Beibei Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Mediator complex as a master regulator of transcription by RNA polymerase II

(2022) William F. Richter et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

BET inhibition disrupts transcription but retains enhancer-promoter contact

(2021) Nicholas T. Crump et al.   Nature Communications

1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells

(2021) Yuji Itoh et al.   Life Science Alliance

The role of liquid–liquid phase separation in regulating enzyme activity

(2021) Brian G. O'Flynn et al.   CURRENT OPINION IN CELL BIOLOGY

Understanding 3D genome organization by multidisciplinary methods

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

Suppression of liquid–liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells

(2021) Sergey V Ulianov et al.   NUCLEIC ACIDS RESEARCH

Transforming eukaryotic cell culture with macromolecular crowding

(2021) Michael Raghunath et al.   TRENDS IN BIOCHEMICAL SCIENCES

Mediator subunit Med15 dictates the conserved “fuzzy” binding mechanism of yeast transcription activators Gal4 and Gcn4

(2021) Lisa M. Tuttle et al.   Nature Communications

Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription

(2021) Megan Palacio et al.   JOURNAL OF MOLECULAR BIOLOGY

Generic nature of the condensed states of proteins

(2021) Monika Fuxreiter et al.   NATURE CELL BIOLOGY

Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin

(2021) Yaojun Zhang et al.   PHYSICAL REVIEW LETTERS

Liquid–Liquid Phase Separation in Chromatin

(2021) Karsten Rippe   Cold Spring Harbor Perspectives in Biology

The Functions of BET Proteins in Gene Transcription of Biology and Diseases

(2021) Ka Lung Cheung et al.   Frontiers in Molecular Biosciences

AlphaFold2-aware protein–DNA binding site prediction using graph transformer

(2021) Qianmu Yuan et al.   BRIEFINGS IN BIOINFORMATICS

Phase separation in transcription factor dynamics and chromatin organization

(2021) Kaustubh Wagh et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates

(2021) Ryanggeun Lee et al.   NUCLEIC ACIDS RESEARCH

What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?

(2021) Julie D. Forman-Kay et al.   RNA

A natural product targets BRD4 to inhibit phase separation and gene transcription

(2021) Cong Wang et al.   iScience

ProNA2020 predicts protein-DNA, protein-RNA and protein-protein binding proteins and residues from sequence

(2020) Jiajun Qiu et al.   JOURNAL OF MOLECULAR BIOLOGY

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Transcription in Living Cells: Molecular Mechanisms of Bursting

(2020) Joseph Rodriguez et al.   Annual Review of Biochemistry

Roles of the BRD4 short isoform in phase separation and active gene transcription

(2020) Xinye Han et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Weak interactions in higher-order chromatin organization

(2020) Omar L Kantidze et al.   NUCLEIC ACIDS RESEARCH

Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components

(2020) Jorge R. Espinosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid–liquid phase separation

(2020) Anne-Marie Ladouceur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence-based engineering of dynamic functions of micrometer-sized DNA droplets

(2020) Yusuke Sato et al.   Science Advances

Liquid–Liquid Phase Separation in Crowded Environments

(2020) Alain A. M. André et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging

(2020) Bo Gu et al.   MOLECULAR CELL

Widespread occurrence of the droplet state of proteins in the human proteome

(2020) Maarten Hardenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Binding and folding in transcriptional complexes

(2020) Ngaio C Smith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2019) Simon Alberti et al.   CELL

Mechanism of DNA-Induced Phase Separation for Transcriptional Repressor VRN1

(2019) Huabin Zhou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

3D genome organization: a role for phase separation and loop extrusion?

(2019) Maike Stam et al.   CURRENT OPINION IN PLANT BIOLOGY

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

Mediator complex interaction partners organize the transcriptional network that defines neural stem cells

(2019) Marti Quevedo et al.   Nature Communications

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

(2019) Mustafa Mir et al.   DEVELOPMENT

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

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

Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation

(2018) Neil O. Robertson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

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

DNA Local-Flexibility-Dependent Assembly of Phase-Separated Liquid Droplets

(2018) Anisha Shakya et al.   BIOPHYSICAL JOURNAL

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

(2018) Ann Boija et al.   CELL

BRD4 and Cancer: going beyond transcriptional regulation

(2018) Benedetta Donati et al.   Molecular Cancer

Nucleosome structure and dynamics are coming of age

(2018) Keda Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SEdb: a comprehensive human super-enhancer database

(2018) Yong Jiang et al.   NUCLEIC ACIDS RESEARCH

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

Biomolecular condensates: organizers of cellular biochemistry

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

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

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

(2017) Tyler S Harmon et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors

(2016) Ngaio C Smith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

(2016) Marton Miskei et al.   NUCLEIC ACIDS RESEARCH

BET Bromodomain Inhibition Releases the Mediator Complex from Select cis -Regulatory Elements

(2016) Anand S. Bhagwat et al.   Cell Reports

RNA Controls PolyQ Protein Phase Transitions

(2015) Huaiying Zhang et al.   MOLECULAR CELL

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SEA: a super-enhancer archive

(2015) Yanjun Wei et al.   NUCLEIC ACIDS RESEARCH

dbSUPER: a database of super-enhancers in mouse and human genome

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

GATA1 directly mediates interactions with closely spaced pseudopalindromic but not distantly spaced double GATA sites on DNA

(2015) Lorna Wilkinson-White et al.   PROTEIN SCIENCE

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(2014) Benoit Ballester et al.   eLife

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

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

(2013) Warren A. Whyte et al.   CELL

Protein Crowding Affects Hydration Structure and Dynamics

(2012) Ryuhei Harada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Macromolecular crowding effects on protein–protein binding affinity and specificity

(2010) Young C. Kim et al.   JOURNAL OF CHEMICAL PHYSICS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes

(2008) Mugdha Bhati et al.   EMBO JOURNAL