An evolutionary perspective of regulatory landscape dynamics in development and disease.

[1]  S. Mundlos,et al.  Structural variation in the 3D genome , 2018, Nature Reviews Genetics.

[2]  S. Rétaux,et al.  Evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation , 2018, Proceedings of the National Academy of Sciences.

[3]  Daniel S. Day,et al.  Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism , 2018, Cell reports.

[4]  V. Corces,et al.  Developing in 3D: the role of CTCF in cell differentiation , 2018, Development.

[5]  N. Shubin,et al.  A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins , 2018, Nature Genetics.

[6]  Daniel S. Day,et al.  YY1 Is a Structural Regulator of Enhancer-Promoter Loops , 2017, Cell.

[7]  Nuno A. Fonseca,et al.  Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.

[8]  B. Lenhard,et al.  Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation , 2017, Nature Communications.

[9]  Erez Lieberman Aiden,et al.  Genome Organization Drives Chromosome Fragility , 2017, Cell.

[10]  Jennifer E. Phillips-Cremins,et al.  YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment , 2017, Genome research.

[11]  P. Rigby,et al.  Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements , 2017, Genome Biology.

[12]  L. Mirny,et al.  Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization , 2017, Cell.

[13]  W. Huber,et al.  The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances , 2016, Developmental cell.

[14]  I. Petersen,et al.  Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking , 2016, Nature Genetics.

[15]  Anthony D. Schmitt,et al.  A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. , 2016, Cell reports.

[16]  S. Mundlos,et al.  Formation of new chromatin domains determines pathogenicity of genomic duplications , 2016, Nature.

[17]  Michael D. Wilson,et al.  Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders , 2016, Genome Biology.

[18]  Jesse R. Dixon,et al.  Chromatin Domains: The Unit of Chromosome Organization. , 2016, Molecular cell.

[19]  L. Mirny,et al.  Formation of Chromosomal Domains in Interphase by Loop Extrusion , 2015, bioRxiv.

[20]  P. Holland,et al.  A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation , 2016, Nature Genetics.

[21]  Daniel S. Day,et al.  Activation of proto-oncogenes by disruption of chromosome neighborhoods , 2015, Science.

[22]  Neva C. Durand,et al.  Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes , 2015, Proceedings of the National Academy of Sciences.

[23]  D. Duboule,et al.  Structure, function and evolution of topologically associating domains (TADs) atHOX loci , 2015, FEBS letters.

[24]  Matthew T. Maurano,et al.  Role of DNA Methylation in Modulating Transcription Factor Occupancy. , 2015, Cell reports.

[25]  Paola Bovolenta,et al.  Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders , 2015, Proceedings of the National Academy of Sciences.

[26]  A. Visel,et al.  Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.

[27]  T. J. Robinson,et al.  An Integrative Breakage Model of genome architecture, reshuffling and evolution , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[28]  Matthieu Muffato,et al.  The 3D organization of chromatin explains evolutionary fragile genomic regions. , 2015, Cell reports.

[29]  D. Odom,et al.  Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture , 2015, Cell reports.

[30]  Jing Liang,et al.  Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.

[31]  M. Valentine,et al.  Modeling of the Human Alveolar Rhabdomyosarcoma Pax3-Foxo1 Chromosome Translocation in Mouse Myoblasts Using CRISPR-Cas9 Nuclease , 2015, PLoS genetics.

[32]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[33]  D. Duboule,et al.  Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci , 2014, Science.

[34]  L. Ettwiller,et al.  Functional and topological characteristics of mammalian regulatory domains , 2014, Genome research.

[35]  Denis Paquette,et al.  Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs , 2013, PLoS genetics.

[36]  D. Duboule,et al.  A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs , 2013, Science.

[37]  Jennifer E. Phillips-Cremins,et al.  Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment , 2013, Cell.

[38]  Sandra Ruf,et al.  An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. , 2013, Developmental cell.

[39]  J. Garcia-Fernández,et al.  Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties , 2012, Scientific Reports.

[40]  J. Sedat,et al.  Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.

[41]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[42]  Wouter de Laat,et al.  A Regulatory Archipelago Controls Hox Genes Transcription in Digits , 2011, Cell.

[43]  Laurence Ettwiller,et al.  Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor , 2011, Nature Genetics.

[44]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[45]  Boris Lenhard,et al.  Genomic regulatory blocks underlie extensive microsynteny conservation in insects. , 2007, Genome research.

[46]  Ivan Ovcharenko,et al.  Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. , 2007, Genome research.

[47]  K. Howe,et al.  Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. , 2007, Genome research.

[48]  Sridhar Hannenhalli,et al.  Recurring genomic breaks in independent lineages support genomic fragility , 2006, BMC Evolutionary Biology.

[49]  Boris Lenhard,et al.  Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes , 2004, BMC Genomics.

[50]  Klaudia Walter,et al.  Open access, freely available online PLoS BIOLOGY Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2022 .

[51]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[52]  I. Amit,et al.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome. , 2009, Science.