Enhancer grammar in development, evolution, and disease: dependencies and interplay

Base-resolution models of transcription-factor binding reveal soft motif syntax

(2021) Žiga Avsec et al.   NATURE GENETICS

Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

(2020) Carlos Perez-Cervantes et al.   DEVELOPMENT

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells

(2020) Dana M King et al.   eLife

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

(2020) Evgeny Z. Kvon et al.   CELL

Cross-species analysis of enhancer logic using deep learning

(2020) Liesbeth Minnoye et al.   GENOME RESEARCH

Index and biological spectrum of human DNase I hypersensitive sites

(2020) Wouter Meuleman et al.   NATURE

Dense and pleiotropic regulatory information in a developmental enhancer

(2020) Timothy Fuqua et al.   NATURE

Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila

(2019) Michelle Pherson et al.   GENOME RESEARCH

Multi-enhancer transcriptional hubs confer phenotypic robustness

(2019) Albert Tsai et al.   eLife

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

(2019) Carl G. de Boer et al.   NATURE BIOTECHNOLOGY

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

(2018) Rui R. Catarino et al.   GENES & DEVELOPMENT

A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites

(2018) Rhea R. Datta et al.   GENES & DEVELOPMENT

Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification

(2018) Jean-François Boisclair Lachance et al.   GENES & DEVELOPMENT

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans

(2018) Pei-Fang Tsai et al.   MOLECULAR CELL

Enhancer Logic and Mechanics in Development and Disease

(2018) Ryan Rickels et al.   TRENDS IN CELL BIOLOGY

Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity

(2018) Arya Zandvakili et al.   PLoS Genetics

The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain

(2018) Ivelisse Cajigas et al.   MOLECULAR CELL

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases

(2018) Marc S. Halfon   TRENDS IN GENETICS

Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements

(2017) Jelena Erceg et al.   GENES & DEVELOPMENT

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

(2017) Michal Levo et al.   MOLECULAR CELL

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

(2017) Jinsen Li et al.   NUCLEIC ACIDS RESEARCH

Systematic dissection of genomic features determining transcription factor binding and enhancer function

(2017) Sharon R. Grossman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

An Enhancer's Length and Composition Are Shaped by Its Regulatory Task

(2017) Lily Li et al.   Frontiers in Genetics

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

(2016) Evgeny Z. Kvon et al.   CELL

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis

(2016) Luis Luna-Zurita et al.   CELL

Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo

(2016) Ezzat El-Sherif et al.   CURRENT BIOLOGY

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Interactions between pluripotency factors specifycis-regulation in embryonic stem cells

(2016) Chris Fiore et al.   GENOME RESEARCH

The appeasement of Doug: a synthetic approach to enhancer biology

(2016) Ben J. Vincent et al.   Integrative Biology

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

How to tune an enhancer

(2016) Scott Barolo   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers

(2016) Emma K. Farley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

(2016) Rupinder Sayal et al.   eLife

An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/Ptch1

(2016) David S Lorberbaum et al.   eLife

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Disentangling Sources of Selection on Exonic Transcriptional Enhancers

(2015) Rachel M. Agoglia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reassessing the “Duon” Hypothesis of Protein Evolution

(2015) Ke Xing et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Theory in Biology: Figure 1 or Figure 7?

(2015) Rob Phillips   TRENDS IN CELL BIOLOGY

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

(2015) Yu Gyoung Tak et al.   Epigenetics & Chromatin

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells

(2014) Felicia SL Ng et al.   NUCLEIC ACIDS RESEARCH

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors

(2013) Soumyadeep Nandi et al.   NUCLEIC ACIDS RESEARCH

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

(2013) Qiong Cheng et al.   PLoS Genetics

Cellular resolution models for even skipped regulation in the entire Drosophila embryo

(2013) Garth R Ilsley et al.   eLife

Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization

(2013) Delphine Menoret et al.   GENOME BIOLOGY

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border

(2012) A. T. Garnett et al.   DEVELOPMENT

Thecis-regulatory code of Hox function inDrosophila

(2012) Sebastian Sorge et al.   EMBO JOURNAL

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Role of Architecture in the Function and Specificity of Two Notch-Regulated Transcriptional Enhancer Modules

(2012) Feng Liu et al.   PLoS Genetics

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

(2011) Scott Barolo   BIOESSAYS

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

(2011) Christina I. Swanson et al.   CURRENT BIOLOGY

Ancestral and conserved cis-regulatory architectures in developmental control genes

(2011) Mark Rebeiz et al.   DEVELOPMENTAL BIOLOGY

Genome-wide identification of conserved regulatory function in diverged sequences

(2011) L. Taher et al.   GENOME RESEARCH

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

A cis-Regulatory Signature in Ascidians and Flies, Independent of Transcription Factor Binding Sites

(2010) Pierre Khoueiry et al.   CURRENT BIOLOGY

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT 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

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

(2010) Richard W. Lusk et al.   PLoS Genetics

Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis

(2009) Y. J. Passamaneck et al.   DEVELOPMENT

Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp

(2009) Lionel Christiaen et al.   DEVELOPMENTAL BIOLOGY

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Organization of developmental enhancers in the Drosophila embryo

(2009) Dmitri Papatsenko et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Michael F. Berger et al.   CELL

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Reverse-Engineering a Transcriptional Enhancer: A Case Study in Drosophila

(2008) Lisa A. Johnson et al.   TISSUE ENGINEERING PART A

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

(2008) Justin Crocker et al.   PLOS BIOLOGY