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

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

(2019) Molly Gasperini et al.   CELL

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

(2018) Daniel R Fuentes et al.   eLife

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

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

(2017) Tyler S Klann et al.   NATURE BIOTECHNOLOGY

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

(2017) Qin Cao et al.   NATURE GENETICS

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

Interrogation of the Atherosclerosis-Associated SORT1 (Sortilin 1) Locus With Primary Human Hepatocytes, Induced Pluripotent Stem Cell-Hepatocytes, and Locus-Humanized Mice

(2017) Xiao Wang et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

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

(2016) Jacob C. Ulirsch et al.   CELL

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

(2016) Ryan Tewhey et al.   CELL

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

(2016) Sakthi D. Moorthy et al.   GENOME RESEARCH

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

(2016) Jesse M. Engreitz et al.   NATURE

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Insight into GATA1 transcriptional activity through interrogation ofciselements disrupted in human erythroid disorders

(2016) Aoi Wakabayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution interrogation of functional elements in the noncoding genome

(2016) N. E. Sanjana et al.   SCIENCE

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes

(2016) Steven Blinka et al.   Cell Reports

Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions

(2015) Jian Xu et al.   MOLECULAR CELL

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

(2015) Sándor Spisák et al.   NATURE MEDICINE

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

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Suhas S.P. Rao et al.   CELL

ASox2distal enhancer cluster regulates embryonic stem cell differentiation potential

(2014) Harry Y. Zhou et al.   GENES & DEVELOPMENT

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

(2014) Yan Li et al.   PLoS One

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Chromatin state maps: new technologies, new insights

(2008) Eric M Mendenhall et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT