Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions

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

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

(2020) Gordana Wutz et al.   eLife

Transcription in Living Cells: Molecular Mechanisms of Bursting

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

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease

(2020) Shaon Basu et al.   CELL

A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning

(2020) Ariel Erijman et al.   MOLECULAR CELL

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

(2020) Svetlana O. Dodonova et al.   NATURE

Phase separation directs ubiquitination of gene-body nucleosomes

(2020) Laura D. Gallego et al.   NATURE

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

(2020) Yi Lu et al.   NATURE CELL BIOLOGY

Selective Mediator dependence of cell-type-specifying transcription

(2020) Martin G. Jaeger et al.   NATURE GENETICS

Mechanisms of OCT4-SOX2 motif readout on nucleosomes

(2020) Alicia K. Michael et al.   SCIENCE

RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

(2020) Porfirio Quintero-Cadena et al.   MOLECULAR CELL

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

Partitioning of cancer therapeutics in nuclear condensates

(2020) Isaac A. Klein et al.   SCIENCE

Single-molecule regulatory architectures captured by chromatin fiber sequencing

(2020) Andrew B. Stergachis et al.   SCIENCE

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Combinatorial Action of Temporally Segregated Transcription Factors

(2020) Julien Charest et al.   DEVELOPMENTAL CELL

LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice

(2019) Kevin Monahan et al.   NATURE

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Active chromatin marks drive spatial sequestration of heterochromatin in C. elegans nuclei

(2019) Daphne S. Cabianca et al.   NATURE

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

(2019) David Trombley McSwiggen et al.   eLife

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes

(2019) Eddie Rodríguez-Carballo et al.   BMC BIOLOGY

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells

(2019) Jieru Li et al.   CELL

Structural Features of Transcription Factors Associating with Nucleosome Binding

(2019) Meilin Fernandez Garcia et al.   MOLECULAR CELL

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

(2019) Laila El Khattabi et al.   CELL

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility

(2019) Diana A. Stavreva et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

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

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

Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor

(2019) Maxime Mivelaz et al.   MOLECULAR CELL

A high‐throughput method to identify trans‐activation domains within transcription factor sequences

(2018) Cosmas D Arnold et al.   EMBO JOURNAL

SRC-3 Coactivator Governs Dynamic Estrogen-Induced Chromatin Looping Interactions during Transcription

(2018) Anil K. Panigrahi et al.   MOLECULAR CELL

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

(2018) Jelle Jacobs et al.   NATURE GENETICS

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain

(2018) Max V. Staller et al.   Cell Systems

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

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

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

(2018) Caroline R. Bartman et al.   MOLECULAR CELL

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

(2018) Mustafa Mir et al.   eLife

Molecular biology: A liquid reservoir for silent chromatin

(2017) Adam Klosin et al.   NATURE

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

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

(2017) Adam G. Larson et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

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

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity

(2015) Rita Gemayel et al.   MOLECULAR CELL

The Mediator complex: a central integrator of transcription

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

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

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

(2012) Tom Sexton et al.   CELL

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

(2012) E. Z. Kvon et al.   GENES & DEVELOPMENT

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

A computational pipeline for comparative ChIP-seq analyses

(2011) Anaïs F Bardet et al.   Nature Protocols

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE