Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

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

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

Decoupling the function of Hox and Shh in developing limb reveals multiple inputs of Hox genes on limb growth

(2013) R. Sheth et al.   DEVELOPMENT

Duplications of hox gene clusters and the emergence of vertebrates

(2013) Natalia Soshnikova et al.   DEVELOPMENTAL BIOLOGY

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

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

(2012) Wulan Deng et al.   CELL

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

(2012) Tom Sexton et al.   CELL

Chromosome organization in the nucleus – charting new territory across the Hi-Cs

(2012) Josée Dostie et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Anterior-posterior differences in HoxD chromatin topology in limb development

(2012) I. Williamson et al.   DEVELOPMENT

Recruitment of 5' Hoxa genes in the allantois is essential for proper extra-embryonic function in placental mammals

(2012) M. Scotti et al.   DEVELOPMENT

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

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

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

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

Landscapes and archipelagos: spatial organization of gene regulation in vertebrates

(2012) Thomas Montavon et al.   TRENDS IN CELL BIOLOGY

Discovering genome regulation with 3C and 3C-related technologies

(2011) Sylvain D. Ethier et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Direct Interactions of OCA-B and TFII-I Regulate Immunoglobulin Heavy-Chain Gene Transcription by Facilitating Enhancer-Promoter Communication

(2011) Xiaodi Ren et al.   MOLECULAR CELL

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

The three-dimensional architecture of Hox cluster silencing

(2010) Maria A. Ferraiuolo et al.   NUCLEIC ACIDS RESEARCH

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

My5C: web tools for chromosome conformation capture studies

(2009) Bryan R Lajoie et al.   NATURE METHODS

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

BAC transgenic analysis reveals enhancers sufficient forHoxa13and neighborhood gene expression in mouse embryonic distal limbs and genital bud

(2008) Jessica A. Lehoczky et al.   EVOLUTION & DEVELOPMENT

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

Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness

(2008) T. Montavon et al.   GENES & DEVELOPMENT

Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes

(2008) Hisashi Miura et al.   NUCLEIC ACIDS RESEARCH

HOXA13 Is Essential for Placental Vascular Patterning and Labyrinth Endothelial Specification

(2008) Carley A. E. Shaut et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY