Towards quantitative analysis of gene regulation by enhancers

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Small genomic insertions form enhancers that misregulate oncogenes

(2017) Brian J. Abraham et al.   Nature Communications

Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae

(2017) Henriette Uthe et al.   Scientific Reports

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Transcriptional Dynamics at Brain Enhancers: from Functional Specialization to Neurodegeneration

(2016) Marit W. Vermunt et al.   Current Neurology and Neuroscience Reports

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

(2016) Alexey K. Shaytan et al.   JOURNAL OF MOLECULAR BIOLOGY

Mediator Undergoes a Compositional Change during Transcriptional Activation

(2016) Natalia Petrenko et al.   MOLECULAR CELL

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Nucleosome-free DNA regions differentially affect distant communication in chromatin

(2016) Ekaterina V. Nizovtseva et al.   NUCLEIC ACIDS RESEARCH

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

(2016) Sergei A. Grigoryev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles

(2016) François Spitz   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The Yin and Yang of Chromatin Dynamics In Stem Cell Fate Selection

(2016) Rene C. Adam et al.   TRENDS IN GENETICS

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Topological Polymorphism of the Two-Start Chromatin Fiber

(2015) Davood Norouzi et al.   BIOPHYSICAL JOURNAL

A brief review of nucleosome structure

(2015) Amber R. Cutter et al.   FEBS LETTERS

Discovering enhancers by mapping chromatin features in primary tissue

(2015) Sarah K. Bowman   GENOMICS

Using transgenic reporter assays to functionally characterize enhancers in animals

(2015) Evgeny Z. Kvon   GENOMICS

Nucleosome positioning and composition modulate in silico chromatin flexibility

(2015) N Clauvelin et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Structural Mechanisms of Nucleosome Recognition by Linker Histones

(2015) Bing-Rui Zhou et al.   MOLECULAR CELL

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

The Mediator complex: a central integrator of transcription

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

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

Inhibition of Super-Enhancer Activity in Autoinflammatory Site-Derived T Cells Reduces Disease-Associated Gene Expression

(2015) Janneke G.C. Peeters et al.   Cell Reports

Structure of a bacterial RNA polymerase holoenzyme open promoter complex

(2015) Brian Bae et al.   eLife

Super Enhancers in Cancers, Complex Disease, and Developmental Disorders

(2015) Adrienne Niederriter et al.   Genes

Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy

(2014) Feng Cui et al.   BMC BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

(2014) Rasika Mundade et al.   CELL CYCLE

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome

(2014) Robert K. McGinty et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Enhancer biology and enhanceropathies

(2014) Edwin Smith 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

Enhanced dissection of the regulatory genome

(2013) Matthew Slattery et al.   NATURE METHODS

TALE-mediated modulation of transcriptional enhancers in vivo

(2013) Justin Crocker et al.   NATURE METHODS

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

(2013) James Q Boedicker et al.   PHYSICAL BIOLOGY

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

(2013) G. Moyle-Heyrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insights into the histone H1-nucleosome complex

(2013) B.-R. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distal enhancers: new insights into heart development and disease

(2013) Joseph A. Wamstad et al.   TRENDS IN CELL BIOLOGY

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

Atomistic simulations of nucleosomes

(2013) Mithun Biswas et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Characterization of Enhancer Function from Genome-Wide Analyses

(2012) Glenn A. Maston et al.   Annual Review of Genomics and Human Genetics

Chromatin domains, insulators, and the regulation of gene expression

(2012) Rodolfo Ghirlando et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

Genome-wide phosphoacetylation of histone H3 atDrosophilaenhancers and promoters

(2012) Wendy A. Kellner et al.   GENOME RESEARCH

Internucleosomal Interactions Mediated by Histone Tails Allow Distant Communication in Chromatin

(2012) Olga I. Kulaeva et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

From cells to chromatin: Capturing snapshots of genome organization with 5C technology

(2012) Maria A. Ferraiuolo et al.   METHODS

Distant Activation of Transcription: Mechanisms of Enhancer Action

(2012) O. I. Kulaeva et al.   MOLECULAR AND CELLULAR BIOLOGY

Functional Association of Gdown1 with RNA Polymerase II Poised on Human Genes

(2012) Bo Cheng et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization

(2012) R. Vafabakhsh et al.   SCIENCE

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Evidence That Gene Activation and Silencing during Stem Cell Differentiation Requires a Transcriptionally Paused Intermediate State

(2011) Jonathan L. Golob et al.   PLoS One

The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere

(2011) H. A. Cole et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators

(2011) S. Mukhopadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions between subunits of the Mediator complex with gene-specific transcription factors

(2011) Tilman Borggrefe et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin

(2010) Anita Scipioni et al.   BIOPHYSICAL CHEMISTRY

Histone Depletion Facilitates Chromatin Loops on the Kilobasepair Scale

(2010) Philipp M. Diesinger et al.   BIOPHYSICAL JOURNAL

Local Geometry and Elasticity in Compact Chromatin Structure

(2010) Elena F. Koslover et al.   BIOPHYSICAL JOURNAL

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

(2010) S. Stella et al.   GENES & DEVELOPMENT

Analysis of Active and Inactive X Chromosome Architecture Reveals the Independent Organization of 30 nm and Large-Scale Chromatin Structures

(2010) Catherine Naughton et al.   MOLECULAR CELL

TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation

(2010) Gabor Papai et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Inducible gene expression: diverse regulatory mechanisms

(2010) Vikki M. Weake et al.   NATURE REVIEWS GENETICS

10 Years of Tension on Chromatin: Results from Single Molecule Force Spectroscopy

(2009) Fan-Tso Chien et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

A Tale of Tails: How Histone Tails Mediate Chromatin Compaction in Different Salt and Linker Histone Environments†

(2009) Gaurav Arya et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle

(2009) Christopher K. Materese et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Shifting Players and Paradigms in Cell-Specific Transcription

(2009) Joseph A. D'Alessio et al.   MOLECULAR CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

(2009) S. A. Grigoryev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb

(2008) S. A. Vokes et al.   GENES & DEVELOPMENT

Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd

(2008) C. Morey et al.   JOURNAL OF CELL SCIENCE

Structure and Regulatory Mechanism of Aquifex aeolicus NtrC4: Variability and Evolution in Bacterial Transcriptional Regulation

(2008) Joseph D. Batchelor et al.   JOURNAL OF MOLECULAR BIOLOGY