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

The Downstream Transcriptional Enhancer, Ed, Positively Regulates Mouse Ig  Gene Expression and Somatic Hypermutation

(2014) Y. Xiang et al.   JOURNAL OF IMMUNOLOGY

Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions

(2011) Robert K Maeda et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

L'enfant terrible at 30: the maturation of evolutionary developmental biology

(2011) E. S. Haag et al.   DEVELOPMENT

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

(2011) L. Dunipace et al.   DEVELOPMENT

Control of Distal-less expression in the Drosophila appendages by functional 3′ enhancers

(2011) Máximo Ibo Galindo et al.   DEVELOPMENTAL BIOLOGY

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

(2011) Nicolás Frankel et al.   NATURE

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

(2011) Noor M Ghiasvand et al.   NATURE NEUROSCIENCE

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo

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

Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element

(2011) Antoine Barrière et al.   PLoS Genetics

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

(2011) Jason A. Watts et al.   PLoS Genetics

Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development

(2010) Amir A Abbasi et al.   BMC DEVELOPMENTAL BIOLOGY

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Gene Regulation: Enhancers Stepping Out of the Shadow

(2010) Oliver Hobert   CURRENT BIOLOGY

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

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

Distinct enhancers at the Pax3 locus can function redundantly to regulate neural tube and neural crest expressions

(2010) Karl R. Degenhardt et al.   DEVELOPMENTAL BIOLOGY

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

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

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

(2010) J. C. Corbo et al.   GENOME RESEARCH

In Vivo Redundant Function of the 3' IgH Regulatory Element HS3b in the Mouse

(2010) A.-G. Bebin et al.   JOURNAL OF IMMUNOLOGY

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Shadow enhancers confer robustness

(2010) Meera Swami   NATURE REVIEWS GENETICS

A Systematic Enhancer Screen Using Lentivector Transgenesis Identifies Conserved and Non-Conserved Functional Elements at the Olig1 and Olig2 Locus

(2010) Marc Friedli et al.   PLoS One

Redundancy and the Evolution of Cis-Regulatory Element Multiplicity

(2010) Tiago Paixão et al.   PLoS Computational Biology

Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species

(2010) Gizem Kalay et al.   PLoS Genetics

Initiator Elements Function to Determine the Activity State of BX-C Enhancers

(2010) Carole Iampietro et al.   PLoS Genetics

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

Comparative genomics of gene regulation—conservation and divergence of cis-regulatory information

(2009) Antonio CA Meireles-Filho et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A cluster of three long-range enhancers directs regional Shh expression in the epithelial linings

(2009) T. Sagai et al.   DEVELOPMENT

Enhancer-promoter communication at the Drosophila engrailed locus

(2009) D. Kwon et al.   DEVELOPMENT

Secondary enhancers synergise with primary enhancers to guarantee fine-tuned muscle gene expression

(2009) Lucia Guerrero et al.   DEVELOPMENTAL BIOLOGY

Cis-regulatory Mutations in the Caenorhabditis elegans Homeobox Gene Locus cog-1 Affect Neuronal Development

(2009) M. M. O'Meara et al.   GENETICS

Deletion of a Genomic Segment Containing the Cardiac Troponin I Gene Knocks Down Expression of the Slow Troponin T Gene and Impairs Fatigue Tolerance of Diaphragm Muscle

(2009) Han-Zhong Feng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster

(2009) Koen J T Venken et al.   NATURE METHODS

A FOXA1-binding enhancer regulates Hoxb13 expression in the prostate gland

(2009) R. P. McMullin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation of enhancer location in divergent insects

(2009) J. Cande et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression of zebrafish pax6b in pancreas is regulated by two enhancers containing highly conserved cis-elements bound by PDX1, PBX and PREP factors

(2008) François M Delporte et al.   BMC DEVELOPMENTAL BIOLOGY

Multiple modular promoter elements drive graded brinker expression in response to the Dpp morphogen gradient

(2008) L.-C. Yao et al.   DEVELOPMENT

Cis-regulatory organization of the Pax6 gene in the ascidian Ciona intestinalis

(2008) Steven Q. Irvine et al.   DEVELOPMENTAL BIOLOGY

BAC transgenic analysis reveals enhancers sufficient forHoxa13and neighborhood gene expression in mouse embryonic distal limbs and genital bud

(2008) Jessica A. Lehoczky et al.   EVOLUTION & DEVELOPMENT

Regulatory divergence modifies limb length between mammals

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

A powerful method combining homologous recombination and site-specific recombination for targeted mutagenesis in Drosophila

(2008) G. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancing Gene Regulation

(2008) G. A. Wray et al.   SCIENCE

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Chorionic enhancer is dispensable for regulated expression of the human renin gene

(2007) Xiyou Zhou et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY