Multiple layers of complexity incis-regulatory regions of developmental genes

Programming of DNA Methylation Patterns

(2012) Howard Cedar et al.   Annual Review of Biochemistry

Optimized conditions for transgenesis of the ascidian Ciona using square wave electroporation

(2012) David A. Vierra et al.   DEVELOPMENT GENES AND EVOLUTION

Lens development depends on a pair of highly conserved Sox21 regulatory elements

(2012) Stefan Pauls et al.   DEVELOPMENTAL BIOLOGY

Enhancers: emerging roles in cell fate specification

(2012) Chin-Tong Ong et al.   EMBO REPORTS

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

(2012) M. Visser et al.   GENOME RESEARCH

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Improved Mos1-mediated transgenesis in C. elegans

(2012) Christian Frøkjær-Jensen et al.   NATURE METHODS

Developmental Regulation of Chromatin Conformation by Hox Proteins in Drosophila

(2012) Marios Agelopoulos et al.   Cell Reports

Polycomb-Like 3 Promotes Polycomb Repressive Complex 2 Binding to CpG Islands and Embryonic Stem Cell Self-Renewal

(2012) Julie Hunkapiller et al.   PLoS Genetics

Genomic Imprinting: A Mammalian Epigenetic Discovery Model

(2011) Denise P. Barlow   Annual Review of Genetics

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

(2011) Scott Barolo   BIOESSAYS

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

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

Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites

(2011) Aaron W. Aday et al.   DEVELOPMENTAL BIOLOGY

CpG island chromatin

(2011) Neil P. Blackledge et al.   Epigenetics

Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge

(2011) D. J. Grau et al.   GENES & DEVELOPMENT

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

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

(2011) Nicolás Frankel et al.   NATURE

CTCF-binding elements mediate control of V(D)J recombination

(2011) Chunguang Guo et al.   NATURE

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

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

(2011) Noor M Ghiasvand et al.   NATURE NEUROSCIENCE

Mouse Transgenesis Identifies Conserved Functional Enhancers and cis-Regulatory Motif in the Vertebrate LIM Homeobox Gene Lhx2 Locus

(2011) Alison P. Lee et al.   PLoS One

DNaseI Hypersensitivity and Ultraconservation Reveal Novel, Interdependent Long-Range Enhancers at the Complex Pax6 Cis-Regulatory Region

(2011) David J. McBride et al.   PLoS One

Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

(2011) L. F. Franchini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Site-specific integrase-mediated transgenesis in mice via pronuclear injection

(2011) B. Tasic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

(2011) Michael Z. Ludwig 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

Complexity of cis-regulatory organization of six3a during forebrain and eye development in zebrafish

(2010) Chung-Hao Chao et al.   BMC DEVELOPMENTAL BIOLOGY

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

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

Pitx2 defines alternate pathways acting through MyoD during limb and somitic myogenesis

(2010) A. L'Honore et al.   DEVELOPMENT

Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors

(2010) Lisa Prazak et al.   DEVELOPMENTAL BIOLOGY

Chromatin insulator and the promoter targeting sequence modulate the timing of long-range enhancer–promoter interactions in the Drosophila embryo

(2010) Qing Lin 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

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

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

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

Epigenetics and gene expression

(2010) E R Gibney et al.   HEREDITY

Multiple enhancers located in a 1-Mb region upstream of POU3F4 promote expression during inner ear development and may be required for hearing

(2010) Silvia Naranjo et al.   HUMAN GENETICS

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Shadow enhancers confer robustness

(2010) Meera Swami   NATURE REVIEWS GENETICS

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

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

(2010) Gizem Kalay et al.   PLoS Genetics

A Vertebrate Polycomb Response Element Governs Segmentation of the Posterior Hindbrain

(2009) Angela Sing et al.   CELL

A MicroRNA Imparts Robustness against Environmental Fluctuation during Development

(2009) Xin Li et al.   CELL

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

(2009) Nathaniel D. Heintzman et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

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

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

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

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Polycomb complexes and epigenetic states

(2008) Yuri B Schwartz et al.   CURRENT OPINION IN CELL BIOLOGY

Molecular Integration of Wingless, Decapentaplegic, and Autoregulatory Inputs into Distalless during Drosophila Leg Development

(2008) Carlos Estella et al.   DEVELOPMENTAL CELL

Exchange of GATA Factors Mediates Transitions in Looped Chromatin Organization at a Developmentally Regulated Gene Locus

(2008) Huie Jing et al.   MOLECULAR CELL

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

(2008) Justin Crocker et al.   PLOS BIOLOGY

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

(2008) Robert Illingworth et al.   PLOS BIOLOGY

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