Evolution of transcription factor binding in metazoans — mechanisms and functional implications

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

(2014) Petra C Schwalie et al.   GENOME BIOLOGY

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

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

(2013) Justin Cotney et al.   CELL

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Comparative genomics as a tool to understand evolution and disease

(2013) J. Alfoldi et al.   GENOME RESEARCH

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Functional anatomy of distant-acting mammalian enhancers

(2013) D. E. Dickel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

(2013) Mathilde Paris et al.   PLoS Genetics

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

(2012) A. J. Stewart et al.   GENETICS

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

(2012) T. E. Reddy et al.   GENOME RESEARCH

Nature and function of insulator protein binding sites in the Drosophila genome

(2012) Y. B. Schwartz et al.   GENOME RESEARCH

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

(2012) X. Zhang et al.   GENOME RESEARCH

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Evolutionary Conservation of Histone Modifications in Mammals

(2012) Y. H. Woo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

Latent Regulatory Potential of Human-Specific Repetitive Elements

(2012) Michelle C. Ward et al.   MOLECULAR CELL

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

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

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

(2012) Tali Raveh-Sadka et al.   NATURE GENETICS

Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression

(2012) Johannes Schödel et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome

(2012) Xiaochun Ni et al.   PLOS BIOLOGY

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

Regulatory Variation Within and Between Species

(2011) Wei Zheng et al.   Annual Review of Genomics and Human Genetics

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

Nuclear Receptor HNF4α Binding Sequences are Widespread in Alu Repeats

(2011) Eugene Bolotin et al.   BMC GENOMICS

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

(2011) Nicolas Chevrier et al.   CELL

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

(2011) Claudia Kutter et al.   NATURE GENETICS

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

(2011) Bin Z. He et al.   PLoS Genetics

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

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

(2010) Maximilian Haeussler et al.   DEVELOPMENTAL BIOLOGY

Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

A CTCF-independent role for cohesin in tissue-specific transcription

(2010) D. Schmidt et al.   GENOME RESEARCH

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Transcription factor binding variation in the evolution of gene regulation

(2010) Robin D. Dowell   TRENDS IN GENETICS

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

(2010) Richard W. Lusk et al.   PLoS Genetics

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Detection of nonneutral substitution rates on mammalian phylogenies

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

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

A Conserved Insulator That Recruits CTCF and Cohesin Exists between the Closely Related but Divergently Regulated Interleukin-3 and Granulocyte-Macrophage Colony-Stimulating Factor Genes

(2009) S. R. Bowers et al.   MOLECULAR AND CELLULAR BIOLOGY

Evolution of the Vertebrate Gene Regulatory Network Controlled by the Transcriptional Repressor REST

(2009) R. Johnson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Deep homology and the origins of evolutionary novelty

(2009) Neil Shubin et al.   NATURE

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Evolution of Regulatory Sequences in 12 Drosophila Species

(2009) Jaebum Kim et al.   PLoS Genetics

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

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

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

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

(2007) D. M. McGaughey et al.   GENOME RESEARCH