Limb development: a paradigm of gene regulation

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

(2016) Evgeny Z. Kvon et al.   CELL

Loss and Re-emergence of Legs in Snakes by Modular Evolution of Sonic hedgehog and HOXD Enhancers

(2016) Francisca Leal et al.   CURRENT BIOLOGY

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

Phenotypic subregions within the split-hand/foot malformation 1 locus

(2016) Malene B. Rasmussen et al.   HUMAN GENETICS

Looking beyond the genes: the role of non-coding variants in human disease

(2016) Malte Spielmann et al.   HUMAN MOLECULAR GENETICS

Modulation of tissue repair by regeneration enhancer elements

(2016) Junsu Kang et al.   NATURE

Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state

(2016) Yacine Kherdjemil et al.   NATURE

FGF8 and SHH substitute for anterior–posterior tissue interactions to induce limb regeneration

(2016) Eugeniu Nacu et al.   NATURE

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

Transcriptomic and epigenomic characterization of the developing bat wing

(2016) Walter L Eckalbar et al.   NATURE GENETICS

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

(2016) Rafael D Acemel et al.   NATURE GENETICS

Novel heterozygous frameshift mutation indistal-less homeobox 5underlies isolated split hand/foot malformation type 1

(2016) Asmat Ullah et al.   PEDIATRICS INTERNATIONAL

Regulatory evolution ofTbx5and the origin of paired appendages

(2016) Noritaka Adachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

(2016) Betty M. Booker et al.   PLoS Genetics

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

(2016) Isabel Guerreiro et al.   eLife

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

(2016) Eric T Domyan et al.   eLife

Genetic basis of hindlimb loss in a naturally occurring vertebrate model

(2016) Emily K. Don et al.   Biology Open

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Epigenetic modification maintains intrinsic limb-cell identity in Xenopus limb bud regeneration

(2015) Shinichi Hayashi et al.   DEVELOPMENTAL BIOLOGY

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes

(2015) Carlos R. Infante et al.   DEVELOPMENTAL CELL

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

(2015) Nicolas Lonfat et al.   FEBS LETTERS

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Whole transcriptome expression profiling of mouse limb tendon development by using RNA-seq

(2015) Han Liu et al.   JOURNAL OF ORTHOPAEDIC RESEARCH

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

RA Acts in a Coherent Feed-Forward Mechanism with Tbx5 to Control Limb Bud Induction and Initiation

(2015) Satoko Nishimoto et al.   Cell Reports

Minor Loops in Major Folds: Enhancer–Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease

(2015) Navneet Matharu et al.   PLoS Genetics

The Relationship between Gene Network Structure and Expression Variation among Individuals and Species

(2015) Karen E. Sears et al.   PLoS Genetics

Mutations Affecting the BHLHA9 DNA-Binding Domain Cause MSSD, Mesoaxial Synostotic Syndactyly with Phalangeal Reduction, Malik-Percin Type

(2014) Sajid Malik et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A chromosomal 5q31.1 gain involvingPITX1causes Liebenberg syndrome

(2014) Deirdre Máire Seoighe et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

HeterozygousDLX5nonsense mutation associated with isolated split-hand/foot malformation with reduced penetrance and variable expressivity in two unrelated families

(2014) Anna Sowińska-Seidler et al.   BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY

Genome-wide identification of signaling center enhancers in the developing limb

(2014) J. E. VanderMeer et al.   DEVELOPMENT

Development of five digits is controlled by a bipartite long-range cis-regulator

(2014) L. A. Lettice et al.   DEVELOPMENT

Exome sequencing reveals a heterozygous DLX5 mutation in a Chinese family with autosomal-dominant split-hand/foot malformation

(2014) Xue Wang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Gene dosage of the transcription factor Fingerin (bHLHA9) affects digit development and links syndactyly to ectrodactyly

(2014) O. Schatz et al.   HUMAN MOLECULAR GENETICS

Next generation sequencing of chromosomal rearrangements in patients with split-hand/split-foot malformation provides evidence forDYNC1I1exonic enhancers ofDLX5/6expression in humans

(2014) Hana Lango Allen et al.   JOURNAL OF MEDICAL GENETICS

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs

(2014) Javier Lopez-Rios et al.   NATURE

Patterning and post-patterning modes of evolutionary digit loss in mammals

(2014) Kimberly L. Cooper et al.   NATURE

Differential Expression of Meis2, Mab21l2 and Tbx3 during Limb Development Associated with Diversification of Limb Morphology in Mammals

(2014) Mengyao Dai et al.   PLoS One

Deep conservation of wrist and digit enhancers in fish

(2014) Andrew R. Gehrke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unique expression patterns of multiple key genes associated with the evolution of mammalian flight

(2014) Z. Wang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

(2014) Joost M. Woltering et al.   PLOS BIOLOGY

A Combination of Activation and Repression by a Colinear Hox Code Controls Forelimb-Restricted Expression of Tbx5 and Reveals Hox Protein Specificity

(2014) Satoko Nishimoto et al.   PLoS Genetics

GATA6 Is a Crucial Regulator of Shh in the Limb Bud

(2014) Elena Kozhemyakina et al.   PLoS Genetics

Sp6 and Sp8 Transcription Factors Control AER Formation and Dorsal-Ventral Patterning in Limb Development

(2014) Endika Haro et al.   PLoS Genetics

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

(2013) Justin Cotney et al.   CELL

Decoupling the function of Hox and Shh in developing limb reveals multiple inputs of Hox genes on limb growth

(2013) R. Sheth et al.   DEVELOPMENT

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

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Liebenberg syndrome is caused by a deletion upstream to the PITX1 gene resulting in transformation of the upper limbs to reflect lower limb characteristics

(2013) Mohammad M. Al-Qattan et al.   GENE

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

Multiple phases of chondrocyte enlargement underlie differences in skeletal proportions

(2013) Kimberly L. Cooper et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

The origin of the tetrapod limb: from expeditions to enhancers

(2013) Igor Schneider et al.   TRENDS IN GENETICS

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

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

HOXA13 and HOXD13 expression during development of the syndactylous digits in the marsupial Macropus eugenii

(2012) Keng Yih Chew et al.   BMC DEVELOPMENTAL BIOLOGY

Hox genes regulate the onset of Tbx5 expression in the forelimb

(2012) C. Minguillon et al.   DEVELOPMENT

Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements

(2012) Carlos R. Infante et al.   DEVELOPMENTAL BIOLOGY

Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly

(2012) Laura A. Lettice et al.   DEVELOPMENTAL CELL

Coding exons function as tissue-specific enhancers of nearby genes

(2012) Ramon Y. Birnbaum et al.   GENOME RESEARCH

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Functional characterization of tissue-specific enhancers in the DLX5/6 locus

(2012) Ramon Y. Birnbaum et al.   HUMAN MOLECULAR GENETICS

Disparate Igf1 Expression and Growth in the Fore- and Hind Limbs of a Marsupial Mammal (Monodelphis domestica)

(2012) KAREN E. SEARS et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes

(2012) Deborah I. Ritter et al.   PLoS One

Pitx1 is necessary for normal initiation of hindlimb outgrowth through regulation of Tbx4 expression and shapes hindlimb morphologies via targeted growth control

(2011) V. Duboc et al.   DEVELOPMENT

cis-regulatory mutations are a genetic cause of human limb malformations

(2011) Julia E. VanderMeer et al.   DEVELOPMENTAL DYNAMICS

Developmental basis of mammalian digit reduction: a case study in pigs

(2011) Karen E. Sears et al.   EVOLUTION & DEVELOPMENT

Enhancer-adoption as a mechanism of human developmental disease

(2011) Laura A. Lettice et al.   HUMAN MUTATION

A Symphony of Regulations Centered onp63to Control Development of Ectoderm-Derived Structures

(2011) Luisa Guerrini et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Duplications ofBHLHA9are associated with ectrodactyly and tibia hemimelia inherited in non-Mendelian fashion

(2011) Eva Klopocki et al.   JOURNAL OF MEDICAL GENETICS

Identification of a novelDLX5mutation in a family with autosomal recessive split hand and foot malformation

(2011) Hanan E Shamseldin et al.   JOURNAL OF MEDICAL GENETICS

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature

(2011) I. Schneider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeated modification of early limb morphogenesis programmes underlies the convergence of relative limb length in Anolis lizards

(2011) T. J. Sanger et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Developmental origins of precocial forelimbs in marsupial neonates

(2010) A. L. Keyte et al.   DEVELOPMENT

Genomic Regions Associated with Dermal Hyperpigmentation, Polydactyly and Other Morphological Traits in the Silkie Chicken

(2010) B. Dorshorst et al.   JOURNAL OF HEREDITY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Divergent transcriptional activities determine limb identity

(2010) Jean-François Ouimette et al.   Nature Communications

Distinct Roles of Hand2 in Initiating Polarity and Posterior Shh Expression during the Onset of Mouse Limb Bud Development

(2010) Antonella Galli et al.   PLoS Genetics

Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus

(2010) Evelyn N. Kouwenhoven et al.   PLoS Genetics

Patched 1 is a crucial determinant of asymmetry and digit number in the vertebrate limb

(2009) N. C. Butterfield et al.   DEVELOPMENT

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Vertebrate limb bud development: moving towards integrative analysis of organogenesis

(2009) Rolf Zeller et al.   NATURE REVIEWS GENETICS

Tbx4/5 gene duplication and the origin of vertebrate paired appendages

(2009) C. Minguillon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Y. F. Chan et al.   SCIENCE

Regulation of Dlx5 and Dlx6 gene expression by p63 is involved in EEC and SHFM congenital limb defects

(2008) N. Lo Iacono et al.   DEVELOPMENT

Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs

(2008) D. B. Menke et al.   DEVELOPMENT

Tri-phasic expression of posterior Hox genes during development of pectoral fins in zebrafish: Implications for the evolution of vertebrate paired appendages

(2008) Daegwon Ahn et al.   DEVELOPMENTAL BIOLOGY

Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

Regulatory divergence modifies limb length between mammals

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

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb

(2008) S. A. Vokes et al.   GENES & DEVELOPMENT

The pectoral fin of Panderichthys and the origin of digits

(2008) Catherine A. Boisvert et al.   NATURE

A second wave of Sonic hedgehog expression during the development of the bat limb

(2008) D. Hockman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA