Current challenges in understanding the role of enhancers in disease

Decoding gene regulation in the fly brain

(2022) Jasper Janssens et al.   NATURE

Sequence determinants of human gene regulatory elements

(2022) Biswajyoti Sahu et al.   NATURE GENETICS

Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation

(2022) Hongbo Yang et al.   NATURE GENETICS

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome

(2022) Miguel Martinez-Ara et al.   MOLECULAR CELL

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

(2022) Bernardo P. de Almeida et al.   NATURE GENETICS

Multiple causal variants underlie genetic associations in humans

(2022) Nathan S. Abell et al.   SCIENCE

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation

(2022) Gerard Llimos et al.   Nature Communications

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

(2022) Joseph M. Replogle et al.   CELL

Compatibility rules of human enhancer and promoter sequences

(2022) Drew T. Bergman et al.   NATURE

Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

(2022) Steven Gazal et al.   NATURE GENETICS

Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements

(2021) Henry F. Thomas et al.   MOLECULAR CELL

Enhancer redundancy in development and disease

(2021) Evgeny Z. Kvon et al.   NATURE REVIEWS GENETICS

Systematic analysis of binding of transcription factors to noncoding variants

(2021) Jian Yan et al.   NATURE

Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes

(2021) Jeremy Schwartzentruber et al.   NATURE GENETICS

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

(2021) Žiga Avsec et al.   NATURE GENETICS

Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

(2021) Gloriia Novikova et al.   Nature Communications

Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases

(2021) Mineto Ota et al.   CELL

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

A map of transcriptional heterogeneity and regulatory variation in human microglia

(2021) Adam M. H. Young et al.   NATURE GENETICS

Testing the super-enhancer concept

(2021) Gerd A. Blobel et al.   NATURE REVIEWS GENETICS

Transcription factors: Bridge between cell signaling and gene regulation

(2021) Paula Weidemüller et al.   PROTEOMICS

Enhancers in disease: molecular basis and emerging treatment strategies

(2021) Annique Claringbould et al.   TRENDS IN MOLECULAR MEDICINE

A functional genomics pipeline identifies pleiotropy and cross-tissue effects within obesity-associated GWAS loci

(2021) Amelia C. Joslin et al.   Nature Communications

Responsible use of polygenic risk scores in the clinic: potential benefits, risks and gaps

(2021) et al.   NATURE MEDICINE

Effective gene expression prediction from sequence by integrating long-range interactions

(2021) Žiga Avsec et al.   NATURE METHODS

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report

(2021) et al.   NEW ENGLAND JOURNAL OF MEDICINE

Asthma-associated genetic variants induce IL33 differential expression through an enhancer-blocking regulatory region

(2021) Ivy Aneas et al.   Nature Communications

Quantitative spatial and temporal assessment of regulatory element activity in zebrafish

(2021) Shipra Bhatia et al.   eLife

The GWAS Diversity Monitor tracks diversity by disease in real time

(2020) Melinda C. Mills et al.   NATURE GENETICS

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

(2020) Evgeny Z. Kvon et al.   CELL

Resolving mechanisms of immune‐mediated disease in primary CD 4 T cells

(2020) Christophe Bourges et al.   EMBO Molecular Medicine

Targeted Perturb-seq enables genome-scale genetic screens in single cells

(2020) Daniel Schraivogel et al.   NATURE METHODS

Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension

(2020) Armando Reyes-Palomares et al.   Nature Communications

Predictive features of gene expression variation reveal mechanistic link with differential expression

(2020) Olga M Sigalova et al.   Molecular Systems Biology

Cross-species regulatory sequence activity prediction

(2020) David R. Kelley   PLoS Computational Biology

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

(2020) Daria Bunina et al.   Cell Systems

Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa

(2020) Suzanne E. de Bruijn et al.   AMERICAN JOURNAL OF HUMAN GENETICS

β-catenin-TCF/LEF signaling promotes steady-state and emergency granulopoiesis via G-CSF receptor upregulation

(2020) Petr Danek et al.   BLOOD

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Chromatin Interactions in Differentiating Keratinocytes Reveal Novel Atopic Dermatitis and Psoriasis-Associated Genes

(2020) Pelin Sahlén et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Practical guide for managing large-scale human genome data in research

(2020) Tomoya Tanjo et al.   JOURNAL OF HUMAN GENETICS

Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells

(2020) Jesper G. S. Madsen et al.   NATURE GENETICS

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

(2020) M. Ryan Corces et al.   NATURE GENETICS

Deep learning of immune cell differentiation

(2020) Alexandra Maslova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

Multiplex chromatin interactions with single-molecule precision

(2019) Meizhen Zheng et al.   NATURE

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs

(2019) Magdalena Laugsch et al.   Cell Stem Cell

Chromatin three-dimensional interactions mediate genetic effects on gene expression

(2019) O. Delaneau et al.   SCIENCE

Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D

(2019) Michael I. Robson et al.   MOLECULAR CELL

High-throughput identification of human SNPs affecting regulatory element activity

(2019) Joris van Arensbergen et al.   NATURE GENETICS

Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo

(2019) Jonathan Hasselmann et al.   NEURON

Actors with Multiple Roles: Pleiotropic Enhancers and the Paradigm of Enhancer Modularity

(2019) Gonzalo Sabarís et al.   TRENDS IN GENETICS

Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases

(2019) Blagoje Soskic et al.   NATURE GENETICS

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Stem-cell-derived human microglia transplanted in mouse brain to study human disease

(2019) Renzo Mancuso et al.   NATURE NEUROSCIENCE

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

Genetic regulatory variation in populations informs transcriptome analysis in rare disease

(2019) Pejman Mohammadi et al.   SCIENCE

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus

(2018) Ping Gao et al.   CELL

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

(2018) Junjie Tony Hua et al.   CELL

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

(2018) Sarah Rennie et al.   NUCLEIC ACIDS RESEARCH

Enhancer Logic and Mechanics in Development and Disease

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

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Power, false discovery rate and Winner’s Curse in eQTL studies

(2018) Qin Qin Huang et al.   NUCLEIC ACIDS RESEARCH

SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression

(2017) Kaixiang Cao et al.   GENES & DEVELOPMENT

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease

(2016) Sumantra Chatterjee et al.   CELL

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

(2016) Claire Redin et al.   NATURE GENETICS

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

(2016) Deborah Hay et al.   NATURE GENETICS

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Deep sequencing of 10,000 human genomes

(2016) Amalio Telenti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

Site- and allele-specific polycomb dysregulation in T-cell leukaemia

(2015) Jean-Marc Navarro et al.   Nature Communications

On the identification of potential regulatory variants within genome wide association candidate SNP sets

(2014) Chih-yu Chen et al.   BMC Medical Genomics

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

A common genetic variant within SCN10A modulates cardiac SCN5A expression

(2014) Malou van den Boogaard et al.   JOURNAL OF CLINICAL INVESTIGATION

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

(2014) Lorenzo Pasquali et al.   NATURE GENETICS

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers

(2014) Rasmus Siersbæk et al.   Cell Reports

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

(2013) Michael N Weedon et al.   NATURE GENETICS

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease

(2012) Scott Smemo et al.   HUMAN MOLECULAR GENETICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

(2009) K. M. Lower et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE