Evolution of transcriptional enhancers and animal diversity

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease

(2013) Scott J. Gratz et al.   GENETICS

Efficient Targeted Mutagenesis in Medaka Using Custom-Designed Transcription Activator-Like Effector Nucleases

(2013) S. Ansai et al.   GENETICS

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

(2013) M. A. Supple et al.   GENOME RESEARCH

Neural Injury Alters Proliferation and Integration of Adult-Generated Neurons in the Dentate Gyrus

(2013) J. V. Perederiy et al.   JOURNAL OF NEUROSCIENCE

The Developmental Brain Gene NPAS3 Contains the Largest Number of Accelerated Regulatory Sequences in the Human Genome

(2013) Gretel B. Kamm et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

(2013) F. S. J. de Souza et al.   MOLECULAR BIOLOGY AND EVOLUTION

Knockout mice created by TALEN-mediated gene targeting

(2013) Young Hoon Sung et al.   NATURE BIOTECHNOLOGY

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

Chromatin and epigenetic features of long-range gene regulation

(2013) N. Harmston et al.   NUCLEIC ACIDS RESEARCH

A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice

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

The mystery of extreme non-coding conservation

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

The structure and evolution ofcis-regulatory regions: theshavenbabystory

(2013) David L. Stern et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Regulation from a distance: long-range control of gene expression in development and disease

(2013) V. van Heyningen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

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

Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster

(2013) A. Glaser-Schmitt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Assessing constraints on the path of regulatory sequence evolution

(2013) W. J. Glassford et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

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

Enhancer turnover and conserved regulatory function in vertebrate evolution

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

Deep conservation of cis-regulatory elements in metazoans

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

Many human accelerated regions are developmental enhancers

(2013) J. A. Capra et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution

(2013) A. I. Ramos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

cis-regulatory change associated with snake body plan evolution

(2013) J. H. Mansfield   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

(2013) Li-En Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine

(2013) I. Guerreiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module

(2013) L. Arnoult et al.   SCIENCE

Homeotic Arm-to-Leg Transformation Associated with Genomic Rearrangements at the PITX1 Locus

(2012) Malte Spielmann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Transposable element recruitments in the mammalian placenta: impacts and mechanisms

(2012) D. Emera et al.   Briefings in Functional Genomics

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Making Limbs from Fins

(2012) Igor Schneider et al.   DEVELOPMENTAL CELL

Hoxd13 Contribution to the Evolution of Vertebrate Appendages

(2012) Renata Freitas et al.   DEVELOPMENTAL CELL

Multiple layers of complexity incis-regulatory regions of developmental genes

(2012) Nicolás Frankel   DEVELOPMENTAL DYNAMICS

The Chromatin Fingerprint of Gene Enhancer Elements

(2012) Gabriel E. Zentner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Hundreds of conserved non-coding genomic regions are independently lost in mammals

(2012) Michael Hiller et al.   NUCLEIC ACIDS RESEARCH

Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs

(2012) Lindsay Cade et al.   NUCLEIC ACIDS RESEARCH

29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome

(2012) Craig B. Lowe et al.   PLoS One

Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution

(2012) N. Frankel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human brain evolution: From gene discovery to phenotype discovery

(2012) T. M. Preuss   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors

(2012) I. K. Sur et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Evolution of a tissue-specific silencer underlies divergence in the expression of pax2 and pax8 paralogues

(2012) Haruki Ochi et al.   Nature Communications

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

(2012) Shoa L. Clarke et al.   PLoS Genetics

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

(2011) Scott Barolo   BIOESSAYS

Enhancer and promoter interactions—long distance calls

(2011) Ivan Krivega et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events

(2011) D. K. Goode et al.   DEVELOPMENT

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Loss-of-Function Mutation in a Repressor Module of Human-Specifically Activated Enhancer HACNS1

(2011) K. Sumiyama et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Cory Y. McLean et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

(2011) Nicolás Frankel et al.   NATURE

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Deletion of a remote enhancer near ATOH7 disrupts retinal neurogenesis, causing NCRNA disease

(2011) Noor M Ghiasvand et al.   NATURE NEUROSCIENCE

Transphyletic conservation of developmental regulatory state in animal evolution

(2011) J. L. Royo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

(2011) L. F. Franchini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences

(2011) M. Rebeiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three Periods of Regulatory Innovation During Vertebrate Evolution

(2011) C. B. Lowe et al.   SCIENCE

optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry

(2011) R. D. Reed et al.   SCIENCE

De Novo Genesis of Enhancers in Vertebrates

(2011) Michael P. Eichenlaub et al.   PLOS BIOLOGY

Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development

(2011) Jonathan Göke et al.   PLoS Computational Biology

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

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

Genome–nuclear lamina interactions and gene regulation

(2010) Jop Kind et al.   CURRENT OPINION IN CELL BIOLOGY

When needles look like hay: How to find tissue-specific enhancers in model organism genomes

(2010) Maximilian Haeussler et al.   DEVELOPMENTAL BIOLOGY

Evidence for a Myotomal Hox/Myf Cascade Governing Nonautonomous Control of Rib Specification within Global Vertebral Domains

(2010) Tânia Vinagre et al.   DEVELOPMENTAL CELL

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

A Pituitary-Specific Enhancer of the POMC Gene with Preferential Activity in Corticotrope Cells

(2010) David Langlais et al.   MOLECULAR ENDOCRINOLOGY

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum

(2009) J. D. Cande et al.   DEVELOPMENT

Axial patterning in snakes and caecilians: Evidence for an alternative interpretation of the Hox code

(2009) Joost M. Woltering et al.   DEVELOPMENTAL BIOLOGY

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Human-specific transcriptional regulation of CNS development genes by FOXP2

(2009) Genevieve Konopka et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

Stepwise Modification of a Modular Enhancer Underlies Adaptation in a Drosophila Population

(2009) M. Rebeiz et al.   SCIENCE

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species

(2008) Sangyun Jeong et al.   CELL

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Regulatory divergence modifies limb length between mammals

(2008) C. J. Cretekos et al.   GENES & DEVELOPMENT

Lactose digestion and the evolutionary genetics of lactase persistence

(2008) Catherine J. E. Ingram et al.   HUMAN GENETICS

Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein

(2008) Yongsu Jeong et al.   NATURE GENETICS

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics