Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

Enhancer redundancy in development and disease

(2021) Evgeny Z. Kvon et al.   NATURE REVIEWS GENETICS

Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

(2021) Elizabeth Ing-Simmons et al.   NATURE GENETICS

Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data

(2020) Noah Dukler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

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

Large distances separate coregulated genes in living Drosophila embryos

(2019) Tyler Heist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates

(2019) Ittai E. Eres et al.   PLoS Genetics

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Enhancer–gene maps in the human and zebrafish genomes using evolutionary linkage conservation

(2019) Yves Clément et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Federico Comoglio et al.   GENOME RESEARCH

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

(2018) Clara Lopes Novo et al.   Cell Reports

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

(2018) Charles G. Danko et al.   Nature Ecology & Evolution

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Author Correction: Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS

(2018) David Z. Pan et al.   Nature Communications

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages

(2018) Stefan Schoenfelder et al.   Nature Communications

Author Correction: Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks

(2018) Mun-Kit Choy et al.   Nature Communications

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

(2017) Emily S. Wong et al.   Nature Communications

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

(2017) Paula Freire-Pritchett et al.   eLife

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

(2017) Camille Berthelot et al.   Nature Ecology & Evolution

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

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

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

(2014) Emily S. Wong et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Landscapes and archipelagos: spatial organization of gene regulation in vertebrates

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

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Enhancer-adoption as a mechanism of human developmental disease

(2011) Laura A. Lettice et al.   HUMAN MUTATION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Long-range regulation is a major driving force in maintaining genome integrity

(2009) Emmanuel Mongin et al.   BMC EVOLUTIONARY BIOLOGY

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

(2009) Claire Lemaitre et al.   BMC GENOMICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics