Homeodomain proteins: an update

Zinc fingers and homeoboxes family in human diseases

(2015) Y Liu et al.   CANCER GENE THERAPY

Cancer cell metabolism and developmental homeodomain/POU domain transcription factors: A connecting link

(2015) Biswa Pratim Das Purkayastha et al.   CANCER LETTERS

Deconvolving the Recognition of DNA Shape from Sequence

(2015) Namiko Abe et al.   CELL

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Hox genes, evo-devo, and the case of the ftz gene

(2015) Leslie Pick   CHROMOSOMA

The open for business model of the bithorax complex in Drosophila

(2015) Robert K. Maeda et al.   CHROMOSOMA

The olive flounder (Paralichthys olivaceus) Pax3 homologues are highly conserved, encode multiple isoforms and show unique expression patterns

(2015) Shuang Jiao et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Diverse functions of KNOX transcription factors in the diploid body plan of plants

(2015) Katsutoshi Tsuda et al.   CURRENT OPINION IN PLANT BIOLOGY

Cellular and molecular insights into Hox protein action

(2015) R. Rezsohazy et al.   DEVELOPMENT

Differential pleiotropy and HOX functional organization

(2015) Lovesha Sivanantharajah et al.   DEVELOPMENTAL BIOLOGY

Toward a New Twist in Hox and TALE DNA-Binding Specificity

(2015) Samir Merabet et al.   DEVELOPMENTAL CELL

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State

(2015) Shilu Amin et al.   DEVELOPMENTAL CELL

Structure, function and evolution of topologically associating domains (TADs) atHOXloci

(2015) Nicolas Lonfat et al.   FEBS LETTERS

Phylogenic analysis revealed an expanded C2H2-homeobox subfamily and expression profiles of C2H2 zinc finger gene family in Verticillium dahliae

(2015) Dianguang Xiong et al.   GENE

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis

(2015) Jürgen Hench et al.   PLoS One

Pax factors in transcription and epigenetic remodelling

(2015) Alexandre Mayran et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/PBC Interaction Mode

(2015) Nicolas Foos et al.   STRUCTURE

Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development

(2015) Virpi Töhönen et al.   Nature Communications

Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo

(2015) Manon Baëza et al.   eLife

The TALE face of Hox proteins in animal evolution

(2015) Samir Merabet et al.   Frontiers in Genetics

Role ofHoxgenes in stem cell differentiation

(2015) Anne Seifert   World Journal of Stem Cells

The animal body plan, the prototypic body segment, and eye evolution

(2015) Walter J. Gehring   EVOLUTION & DEVELOPMENT

Function and Evolutionary Origin of Unicellular Camera-Type Eye Structure

(2015) Shiho Hayakawa et al.   PLoS One

The role of WOX genes in flower development

(2014) Enrico Costanzo et al.   ANNALS OF BOTANY

Shared functions of plant and mammalian StAR-related lipid transfer (START) domains in modulating transcription factor activity

(2014) Kathrin Schrick et al.   BMC BIOLOGY

Walter Gehring (1939–2014)

(2014) Eric Wieschaus et al.   CURRENT BIOLOGY

Obituary: Walter J. Gehring (1939-2014)

(2014) A. F. Schier   DEVELOPMENT

Andrés Carrasco (1946–2014)

(2014) Bruce Blumberg   DEVELOPMENTAL BIOLOGY

Walter J. Gehring (1939–2014)

(2014) Marek Mlodzik et al.   DEVELOPMENTAL BIOLOGY

The role of homeobox genes in retinal development and disease

(2014) Jamie L. Zagozewski et al.   DEVELOPMENTAL BIOLOGY

Walter Jakob Gehring (1939–2014)

(2014) Markus Affolter et al.   DEVELOPMENTAL CELL

Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

(2014) Nathalie Feiner et al.   Genome Biology and Evolution

Crystal Structure of the Ubiquitin-like Domain-CUT Repeat-like Tandem of Special AT-rich Sequence Binding Protein 1 (SATB1) Reveals a Coordinating DNA-binding Mechanism

(2014) Zheng Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment

(2014) Ronny Brandt et al.   Journal of Integrative Plant Biology

Enigmatic Orthology Relationships between Hox Clusters of the African Butterfly Fish and Other Teleosts Following Ancient Whole-Genome Duplication

(2014) Kyle J. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

(2014) Sofia A. V. Fortunato et al.   NATURE

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

LIM homeobox transcription factors, a novel subfamily which plays an important role in cancer (Review)

(2014) XI WANG et al.   ONCOLOGY REPORTS

Walter Jakob Gehring: A master of developmental biology

(2014) M. Affolter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Walter Gehring (1939-2014)

(2014) M. Levine   SCIENCE

Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci

(2014) N. Lonfat et al.   SCIENCE

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

(2014) Shengfeng Huang et al.   Nature Communications

Ancient Expansion of the Hox Cluster in Lepidoptera Generated Four Homeobox Genes Implicated in Extra-Embryonic Tissue Formation

(2014) Laura Ferguson et al.   PLoS Genetics

The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription

(2014) Aamna Kaul et al.   PLoS Genetics

Drosophila melanogaster Hox Transcription Factors Access the RNA Polymerase II Machinery through Direct Homeodomain Binding to a Conserved Motif of Mediator Subunit Med19

(2014) Muriel Boube et al.   PLoS Genetics

The Hox-TALE has been wagging for a long time

(2014) David EK Ferrier   eLife

Molecular insights into the origin of the Hox-TALE patterning system

(2014) Bruno Hudry et al.   eLife

START ships lipids across interorganelle space

(2013) Fabien Alpy et al.   BIOCHIMIE

Time is of the essence for ParaHox homeobox gene clustering

(2013) Myles Garstang et al.   BMC BIOLOGY

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

TALE transcription factors during early development of the vertebrate brain and eye

(2013) Dorothea Schulte et al.   DEVELOPMENTAL DYNAMICS

Control of Drosophila embryo patterning by transcriptional co-regulators

(2013) Mattias Mannervik   EXPERIMENTAL CELL RESEARCH

SLIDE, the Protein Interacting Domain of ISWI Remodelers, Binds DDT-domain Proteins of Different Subfamilies in Chromatin Remodeling Complexes

(2013) Jiaqiang Dong et al.   Journal of Integrative Plant Biology

Human HOX gene disorders

(2013) Shane C. Quinonez et al.   MOLECULAR GENETICS AND METABOLISM

The genomes of four tapeworm species reveal adaptations to parasitism

(2013) Isheng J. Tsai et al.   NATURE

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

Structure-function analyses of the human SIX1–EYA2 complex reveal insights into metastasis and BOR syndrome

(2013) Aaron N Patrick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Covariation between homeodomain transcription factors and the shape of their DNA binding sites

(2013) Iris Dror et al.   NUCLEIC ACIDS RESEARCH

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

A Genome-Wide Survey of Genes Encoding Transcription Factors in the Japanese Pearl Oyster,Pinctada fucata: I. Homeobox Genes

(2013) Yoshiaki Morino et al.   ZOOLOGICAL SCIENCE

Sequencing of Pax6 Loci from the Elephant Shark Reveals a Family of Pax6 Genes in Vertebrate Genomes, Forged by Ancient Duplications and Divergences

(2013) Vydianathan Ravi et al.   PLoS Genetics

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

(2013) Michael Clarke et al.   GENOME BIOLOGY

Hox transcriptional specificity despite a single class of cofactors: Are flexible interaction modes the key?

(2012) Samir Merabet et al.   BIOESSAYS

The HARE-HTH and associated domains

(2012) L. Aravind et al.   CELL CYCLE

Evolution of DUX gene macrosatellites in placental mammals

(2012) Andreas Leidenroth et al.   CHROMOSOMA

PAX Proteins and Fables of Their Reconstruction

(2012) Darrell Alan Underhill   CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION

Ghost Loci Imply Hox and ParaHox Existence in the Last Common Ancestor of Animals

(2012) Olivia Mendivil Ramos et al.   CURRENT BIOLOGY

Dimer formation via the homeodomain is required for function and specificity of Sex combs reduced in Drosophila

(2012) Dimitrios K. Papadopoulos et al.   DEVELOPMENTAL BIOLOGY

Exploring the DNA-recognition potential of homeodomains

(2012) S. W. Chu et al.   GENOME RESEARCH

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor

(2012) Yubing Liu et al.   NUCLEIC ACIDS RESEARCH

The structural basis for the oligomerization of the N-terminal domain of SATB1

(2012) Zheng Wang et al.   NUCLEIC ACIDS RESEARCH

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

Sequencing and Analysis of the Mediterranean Amphioxus (Branchiostoma lanceolatum) Transcriptome

(2012) Silvan Oulion et al.   PLoS One

Evolutionarily conserved repressive activity of WOX proteins mediates leaf blade outgrowth and floral organ development in plants

(2012) H. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolution of vision

(2012) Walter J. Gehring   Wiley Interdisciplinary Reviews-Developmental Biology

Evolution of homeobox genes

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

The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages

(2011) Ying-fu Zhong et al.   BMC EVOLUTIONARY BIOLOGY

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Pbx homeodomain proteins: TALEnted regulators of limb patterning and outgrowth

(2011) Terence D. Capellini et al.   DEVELOPMENTAL DYNAMICS

EAR motif-mediated transcriptional repression in plants

(2011) Sateesh Kagale et al.   Epigenetics

HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology

(2011) Ying-fu Zhong et al.   EVOLUTION & DEVELOPMENT

The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein

(2011) K. H. Wong et al.   GENES & DEVELOPMENT

Nkx2.2 repressor complex regulates islet  -cell specification and prevents  -to- -cell reprogramming

(2011) J. B. Papizan et al.   GENES & DEVELOPMENT

New insights from hemichordate genomes: prebilaterian origin and parallel modifications in the paired domain of the Pax gene eyegone

(2011) Markus Friedrich et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

A Per-ARNT-Sim-Like Sensor Domain Uniquely Regulates the Activity of the Homeodomain Leucine Zipper Transcription Factor REVOLUTA inArabidopsis

(2011) Enrico Magnani et al.   PLANT CELL

Evolution of Invertebrate Deuterostomes and Hox/ParaHox Genes

(2011) Tetsuro Ikuta   GENOMICS PROTEOMICS & BIOINFORMATICS

Early evolution of the LIM homeobox gene family

(2010) Mansi Srivastava et al.   BMC BIOLOGY

A family history of DUX4: phylogenetic analysis of DUXA, B, C and Duxbl reveals the ancestral DUX gene

(2010) Andreas Leidenroth et al.   BMC EVOLUTIONARY BIOLOGY

KNOX genes: versatile regulators of plant development and diversity

(2010) A. Hay et al.   DEVELOPMENT

Origin of Pax and Six gene families in sponges: Single PaxB and Six1/2 orthologs in Chalinula loosanoffi

(2010) April Hill et al.   DEVELOPMENTAL BIOLOGY

Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression oftshz2andtshz3bin the zebrafish

(2010) Joana S. Santos et al.   DEVELOPMENTAL DYNAMICS

Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster

(2010) Jerome H. L. Hui et al.   EVOLUTION & DEVELOPMENT

Identification and characterization ofNasoniaPax genes

(2010) R. G. Keller et al.   INSECT MOLECULAR BIOLOGY

A Novel Pax-like Protein Involved in Transcriptional Activation of Cyst Wall Protein Genes inGiardia lamblia

(2010) Yi-Ting Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Arabidopsis shoot organogenesis is enhanced by an amino acid change in the ATHB15 transcription factor

(2010) J. Duclercq et al.   PLANT BIOLOGY

Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish

(2010) H. Suga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rhox genes

(2010) James A MacLean et al.   REPRODUCTION

A conserved cluster of three PRD-class homeobox genes (homeobrain, rx and orthopedia) in the Cnidaria and Protostomia

(2010) Maureen E Mazza et al.   EvoDevo

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

(2010) Joseph F Ryan et al.   EvoDevo

Classification of sequence signatures: a guide to Hox protein function

(2009) Samir Merabet et al.   BIOESSAYS

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

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

The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication

(2009) Shigehiro Kuraku et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes

(2009) K. Mukherjee et al.   MOLECULAR BIOLOGY AND EVOLUTION

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Arabidopsis WUSCHEL Is a Bifunctional Transcription Factor That Acts as a Repressor in Stem Cell Regulation and as an Activator in Floral Patterning

(2009) M. Ikeda et al.   PLANT CELL

The WUS homeobox-containing (WOX) protein family

(2009) Eric van der Graaff et al.   GENOME BIOLOGY

A Lexicon for Homeodomain-DNA Recognition

(2008) Markus Affolter et al.   CELL

Early Sexual Origins of Homeoprotein Heterodimerization and Evolution of the Plant KNOX/BELL Family

(2008) Jae-Hyeok Lee et al.   CELL

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

The sine oculis homeobox (SIX) family of transcription factors as regulators of development and disease

(2008) J. P. Kumar   CELLULAR AND MOLECULAR LIFE SCIENCES

Context-dependent regulation of Groucho/TLE-mediated repression

(2008) Einat Cinnamon et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae

(2008) Naohito Takatori et al.   DEVELOPMENT GENES AND EVOLUTION

Evolution of CUT class homeobox genes: insights from the genome of the amphioxus, Branchiostoma floridae

(2008) Naohito Takatori et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Phylogenetic Analysis of the Plant-specificZinc Finger-HomeoboxandMini Zinc FingerGene Families

(2008) Wei Hu et al.   Journal of Integrative Plant Biology

Recurrent Tandem Gene Duplication Gave Rise to Functionally Divergent Genes in Drosophila

(2008) C. Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Homeodomain-leucine Zipper II gene family: diversity and redundancy

(2008) Angela Raffaella Ciarbelli et al.   PLANT MOLECULAR BIOLOGY

Groucho/Tup1 family co-repressors in plant development

(2008) Zhongchi Liu et al.   TRENDS IN PLANT SCIENCE

The Groucho/TLE/Grg family of transcriptional co-repressors

(2008) Barbara H Jennings et al.   GENOME BIOLOGY

PBX proteins: much more than Hox cofactors

(2007) Audrey Laurent et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY