Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

(2017) Paula Freire-Pritchett et al.   eLife

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model

(2016) N. K. Wilson et al.   BLOOD

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Coordinating cell proliferation and differentiation: Antagonism between cell cycle regulators and cell type-specific gene expression

(2016) Suzan Ruijtenberg et al.   CELL CYCLE

Dissection of transcriptional andcis‐regulatory control of differentiation in human pancreatic cancer

(2016) Giuseppe R Diaferia et al.   EMBO JOURNAL

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

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Interactions between pluripotency factors specifycis-regulation in embryonic stem cells

(2016) Chris Fiore et al.   GENOME RESEARCH

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

A Simple Grammar Defines Activating and Repressing cis -Regulatory Elements in Photoreceptors

(2016) Michael A. White et al.   Cell Reports

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Hematopoietic stem cells: concepts, definitions, and the new reality

(2015) C. J. Eaves   BLOOD

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

(2015) Elizabeth Ing-Simmons et al.   GENOME RESEARCH

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Super-enhancers delineate disease-associated regulatory nodes in T cells

(2015) Golnaz Vahedi et al.   NATURE

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

(2015) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

ZEB1 and TCF4 reciprocally modulate their transcriptional activities to regulate Wnt target gene expression

(2015) E Sánchez-Tilló et al.   ONCOGENE

Unipotent Megakaryopoietic Pathway Bridging Hematopoietic Stem Cells and Mature Megakaryocytes

(2015) Hidekazu Nishikii et al.   STEM CELLS

High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

(2015) Federico Comoglio et al.   Cell Reports

Sox2 acts as a transcriptional repressor in neural stem cells

(2014) Yu-Ru Liu et al.   BMC NEUROSCIENCE

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

(2014) Eirene Markenscoff-Papadimitriou et al.   CELL

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

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

Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila

(2014) Federico Comoglio et al.   PLoS Computational Biology

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

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling

(2013) A. Eijkelenboom et al.   Molecular Systems Biology

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

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

(2012) Tom Sexton et al.   CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   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

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

(2012) Yin C Lin et al.   NATURE IMMUNOLOGY

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Hematopoiesis

(2012) M. A. Rieger et al.   Cold Spring Harbor Perspectives in Biology

Genomic and Biochemical Insights into the Specificity of ETS Transcription Factors

(2011) Peter C. Hollenhorst et al.   Annual Review of Biochemistry

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Thrombopoietin and hematopoietic stem cells

(2011) Carolyn A. de Graaf et al.   CELL CYCLE

Critical roles for c-Myb in lymphoid priming and early B-cell development

(2010) K. T. Greig et al.   BLOOD

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adult Hematopoietic Stem and Progenitor Cells Require Either Lyl1 or Scl for Survival

(2009) George P. Souroullas et al.   Cell Stem Cell

Sumoylation of the Transcription Factor NFATc1 Leads to Its Subnuclear Relocalization and Interleukin-2 Repression by Histone Deacetylase

(2009) Arnab Nayak et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

c-Myb Is Required for Pro-B Cell Differentiation

(2009) S. P. Fahl et al.   JOURNAL OF IMMUNOLOGY

Regulation of megakaryocyte maturation and platelet formation

(2009) D. BLUTEAU et al.   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Conditional c-myb knockout in adult hematopoietic stem cells leads to loss of self-renewal due to impaired proliferation and accelerated differentiation

(2009) Y. K. Lieu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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