Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

(2016) Vahan B. Indjeian et al.   CELL

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework

(2016) Ignacio Maeso et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2015) Darío G. Lupiáñez et al.   CELL

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)

(2015) Elisa Giorgio et al.   HUMAN MOLECULAR GENETICS

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

(2015) Carlos Gómez-Marín et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Complete re-sequencing of a 2Mb topological domain encompassing the FTO/IRXB genes identifies a novel obesity-associated region upstream of IRX5

(2015) Lilian E. Hunt et al.   Genome Medicine

depmixS4: AnRPackage for Hidden Markov Models

(2015) Ingmar Visser et al.   Journal of Statistical Software

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

(2014) Suhas S.P. Rao et al.   CELL

Mapping the Shh long-range regulatory domain

(2014) E. Anderson et al.   DEVELOPMENT

A survey of ancient conserved non-coding elements in the PAX6 locus reveals a landscape of interdigitated cis-regulatory archipelagos

(2014) Shipra Bhatia et al.   DEVELOPMENTAL BIOLOGY

Restless Legs Syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon

(2014) D. Spieler et al.   GENOME RESEARCH

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

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

(2014) Muhammad A. Zabidi et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

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

(2014) Scott Smemo et al.   NATURE

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci

(2014) N. Lonfat et al.   SCIENCE

The mystery of extreme non-coding conservation

(2013) N. Harmston et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

(2013) Emily V. Chambers et al.   PLoS Computational Biology

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

(2012) Tom Sexton et al.   CELL

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

(2012) I. Maeso et al.   GENOME RESEARCH

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

(2012) M. Irimia et al.   GENOME RESEARCH

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Identification and Analysis of Conserved cis-Regulatory Regions of the MEIS1 Gene

(2012) José Luis Royo et al.   PLoS One

Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties

(2012) Manuel Irimia et al.   Scientific Reports

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

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions

(2011) José Luis Royo et al.   PLoS One

Three Periods of Regulatory Innovation During Vertebrate Evolution

(2011) C. B. Lowe et al.   SCIENCE

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation

(2011) Juan J. Tena et al.   Nature Communications

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity

(2010) Deborah I. Ritter et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3

(2009) A. Ragvin 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

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

(2009) Xianjun Dong et al.   GENOME BIOLOGY

Transcriptional features of genomic regulatory blocks

(2009) Altuna Akalin et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes

(2008) Pavla Navratilova et al.   DEVELOPMENTAL BIOLOGY

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

(2008) Pär G Engström et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY