Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes

(2014) J. C. Perez et al.   GENES & DEVELOPMENT

Deep Vertebrate Roots for Mammalian Zinc Finger Transcription Factor Subfamilies

(2014) Hui Liu et al.   Genome Biology and Evolution

Tempo and mode of regulatory evolution in Drosophila

(2014) J. D. Coolon et al.   GENOME RESEARCH

Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks

(2014) Alys M. Cheatle Jarvela et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification of Transcription Factor Paralogs via Noncanonical Modularity in C2H2 Zinc Finger DNA Binding

(2014) Trevor Siggers et al.   MOLECULAR CELL

A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity

(2014) C. Sayou et al.   SCIENCE

Post-translational modification networks regulating FOXP3 function

(2014) Jorg van Loosdregt et al.   TRENDS IN IMMUNOLOGY

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

Evolution of transcriptional enhancers and animal diversity

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

Global and Stage Specific Patterns of Krüppel-Associated-Box Zinc Finger Protein Gene Expression in Murine Early Embryonic Cells

(2013) Andrea Corsinotti et al.   PLoS One

DNA-binding specificity changes in the evolution of forkhead transcription factors

(2013) S. Nakagawa 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

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

(2013) A. de Mendoza et al.   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

Recurrent Modification of a Conserved Cis-Regulatory Element Underlies Fruit Fly Pigmentation Diversity

(2013) William A. Rogers et al.   PLoS Genetics

Gains of ubiquitylation sites in highly conserved proteins in the human lineage

(2012) Dong Seon Kim et al.   BMC BIOINFORMATICS

Induction of the neural crest state: Control of stem cell attributes by gene regulatory, post-transcriptional and epigenetic interactions

(2012) Maneeshi S. Prasad et al.   DEVELOPMENTAL BIOLOGY

Coral Comparative Genomics Reveal Expanded Hox Cluster in the Cnidarian-Bilaterian Ancestor

(2012) T. Q. DuBuc et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

A Recent Evolutionary Change Affects a Regulatory Element in the Human FOXP2 Gene

(2012) Tomislav Maricic et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Diversification of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization

(2012) Bernard J. Koch et al.   PLoS One

The KRAB-ZFP/KAP1 System Contributes to the Early Embryonic Establishment of Site-Specific DNA Methylation Patterns Maintained during Development

(2012) Simon Quenneville et al.   Cell Reports

Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors

(2012) Geeta N. Eick et al.   PLoS Genetics

Evolution of homeobox genes

(2012) Peter W. H. Holland   Wiley Interdisciplinary Reviews-Developmental Biology

Duplication and maintenance of the Myb genes of vertebrate animals

(2012) C. J. Davidson et al.   Biology Open

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

(2011) Vincent J. Lynch et al.   NATURE

Gain, Loss and Divergence in Primate Zinc-Finger Genes: A Rich Resource for Evolution of Gene Regulatory Differences between Species

(2011) Katja Nowick et al.   PLoS One

Evolution of a derived protein–protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation

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

Extensive DNA-binding specificity divergence of a conserved transcription regulator

(2011) C. R. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

(2011) Raluca Gordân et al.   GENOME BIOLOGY

Early evolution of the LIM homeobox gene family

(2010) Mansi Srivastava et al.   BMC BIOLOGY

Lineage-specific transcription factors and the evolution of gene regulatory networks

(2010) K. Nowick et al.   Briefings in Functional Genomics

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity

(2010) S. Rowan et al.   GENES & DEVELOPMENT

Massive turnover of functional sequence in human and other mammalian genomes

(2010) S. Meader et al.   GENOME RESEARCH

Unexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzaki

(2010) A. Sebe-Pedros et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Surprising flexibility in a conserved Hox transcription factor over 550 million years of evolution

(2010) A. Heffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) D. Schmidt et al.   SCIENCE

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

(2009) Christian A. Grove et al.   CELL

Early evolution of metazoan transcription factors

(2009) Bernard M Degnan et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Functional equivalence of the zinc finger transcription factors Osr1 and Osr2 in mouse development

(2009) Yang Gao et al.   DEVELOPMENTAL BIOLOGY

A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos

(2009) Brenna S. McCauley et al.   DEVELOPMENTAL BIOLOGY

Sex-specific and lineage-specific alternative splicing in primates

(2009) R. Blekhman et al.   GENOME RESEARCH

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Domain shuffling and the evolution of vertebrates

(2009) T. Kawashima et al.   GENOME RESEARCH

HoxA-11 and FOXO1A Cooperate to Regulate Decidual Prolactin Expression: Towards Inferring the Core Transcriptional Regulators of Decidual Genes

(2009) Vincent J. Lynch et al.   PLoS One

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain

(2009) Katja Nowick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

The metazoan history of the COE transcription factors. Selection of a variant HLH motif by mandatory inclusion of a duplicated exon in vertebrates

(2008) Virginie Daburon et al.   BMC EVOLUTIONARY BIOLOGY

The Regulation and Evolution of a Genetic Switch Controlling Sexually Dimorphic Traits in Drosophila

(2008) Thomas M. Williams et al.   CELL

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

(2008) Sean B. Carroll   CELL

Context-dependent regulation of Hox protein functions by CK2 phosphorylation sites

(2008) Ouarda Taghli-Lamallem et al.   DEVELOPMENT GENES AND EVOLUTION

Neuronal function of Tbx20 conserved from nematodes to vertebrates

(2008) Roger Pocock et al.   DEVELOPMENTAL BIOLOGY

Evolution of an insect-specific GROUCHO-interaction motif in the ENGRAILED selector protein

(2008) Chris Todd Hittinger et al.   EVOLUTION & DEVELOPMENT

Sox12 Deletion in the Mouse Reveals Nonreciprocal Redundancy with the Related Sox4 and Sox11 Transcription Factors

(2008) M. Hoser et al.   MOLECULAR AND CELLULAR BIOLOGY

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals

(2008) V. J. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA