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

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

(2019) Molly Gasperini et al.   CELL

Systematic interrogation of human promoters

(2019) Shira Weingarten-Gabbay et al.   GENOME RESEARCH

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

(2019) Wai Lim Ku et al.   NATURE METHODS

Profiling of Pluripotency Factors in Single Cells and Early Embryos

(2019) Sarah J. Hainer et al.   CELL

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

(2019) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Dynamic genetic regulation of gene expression during cellular differentiation

(2019) B. J. Strober et al.   SCIENCE

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

(2019) Jason C. Klein et al.   Nature Communications

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

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

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

(2019) Dong-Sung Lee et al.   NATURE METHODS

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

(2019) Judhajeet Ray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

(2019) Martin Kircher et al.   Nature Communications

Identifying Novel Enhancer Elements with CRISPR-Based Screens

(2018) Jason C. Klein et al.   ACS Chemical Biology

Prediction of enhancer-promoter interactions via natural language processing

(2018) Wanwen Zeng et al.   BMC GENOMICS

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

(2018) Ryan Tewhey et al.   CELL

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

(2018) Monique G. P. van der Wijst et al.   NATURE GENETICS

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Principles of Chromosome Architecture Revealed by Hi-C

(2018) Kyle P. Eagen   TRENDS IN BIOCHEMICAL SCIENCES

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

(2018) Charles G. Danko et al.   Nature Ecology & Evolution

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

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

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

Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies

(2018) Carsten Bahr et al.   NATURE

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Publisher Correction: Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing

(2018) Binbin Lai et al.   NATURE

A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity

(2018) Brett B Maricque et al.   NATURE BIOTECHNOLOGY

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers

(2018) Jacob M. Tome et al.   NATURE GENETICS

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

(2018) Xinchen Wang et al.   Nature Communications

The punctilious RNA polymerase II core promoter

(2017) Long Vo ngoc et al.   GENES & DEVELOPMENT

Dynamic assembly and activation of estrogen receptor α enhancers through coregulator switching

(2017) Shino Murakami et al.   GENES & DEVELOPMENT

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Intragenic Enhancers Attenuate Host Gene Expression

(2017) Senthilkumar Cinghu et al.   MOLECULAR CELL

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

DNA sequencing at 40: past, present and future

(2017) Jay Shendure et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

(2017) Tyler S Klann et al.   NATURE BIOTECHNOLOGY

Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability

(2017) Ryan Rickels et al.   NATURE GENETICS

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

(2017) Yarui Diao et al.   NATURE METHODS

Resolving systematic errors in widely used enhancer activity assays in human cells

(2017) Felix Muerdter et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan 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

PAF1 regulation of promoter-proximal pause release via enhancer activation

(2017) Fei Xavier Chen et al.   SCIENCE

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

(2017) Anniina Vihervaara et al.   Nature Communications

Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein

(2017) Yong Lei et al.   Nature Communications

Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

(2017) Deborah Y. Kwon et al.   Nature Communications

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

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

(2017) Lily Li et al.   Frontiers in Genetics

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

(2016) Damian Smedley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

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

(2016) Iain Williamson et al.   DEVELOPMENT

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

(2016) Yarui Diao et al.   GENOME RESEARCH

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Genome-wide mapping of autonomous promoter activity in human cells

(2016) Joris van Arensbergen et al.   NATURE BIOTECHNOLOGY

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

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

The power of multiplexed functional analysis of genetic variants

(2016) Molly Gasperini et al.   Nature Protocols

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

High-resolution interrogation of functional elements in the noncoding genome

(2016) N. E. Sanjana et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

CRISPR Screens to Discover Functional Noncoding Elements

(2016) Jason B. Wright et al.   TRENDS IN GENETICS

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs

(2015) Estel Aparicio-Prat et al.   BMC GENOMICS

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

(2015) Darío G. Lupiáñez et al.   CELL

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

(2015) Christopher M. Vockley et al.   GENOME RESEARCH

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Functional footprinting of regulatory DNA

(2015) Jeff Vierstra et al.   NATURE METHODS

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

(2015) Dhawal Jain et al.   NUCLEIC ACIDS RESEARCH

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

(2014) Yuexin Zhou et al.   NATURE

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

(2014) Wenxiu Ma et al.   NATURE METHODS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

(2013) Waseem Akhtar et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Supercoiling in DNA and chromatin

(2013) Nick Gilbert et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

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

(2013) Robin P Smith et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Anterior-posterior differences in HoxD chromatin topology in limb development

(2012) I. Williamson et al.   DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

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

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

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

(2012) Stefan Bonn et al.   NATURE GENETICS

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

(2012) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Patterns of Cis Regulatory Variation in Diverse Human Populations

(2012) Barbara E. Stranger et al.   PLoS Genetics

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Insulators and promoters: closer than we think

(2010) Jesse R. Raab et al.   NATURE REVIEWS GENETICS

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Computational methods for the detection of cis-regulatory modules

(2009) P. Van Loo et al.   BRIEFINGS IN BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

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

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

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE