Enhancer RNAs predict enhancer–gene regulatory links and are critical for enhancer function in neuronal systems

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

(2020) Kailong Li et al.   Nature Communications

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

(2019) Molly Gasperini et al.   CELL

Genomic Enhancers in Brain Health and Disease

(2019) Nancy V.N. Carullo et al.   Genes

Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes

(2019) Liang-Fu Chen et al.   Cell Reports

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

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

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

(2019) Michael Song et al.   NATURE GENETICS

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

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

Dynamic lineage priming is driven via direct enhancer regulation by ERK

(2019) William B. Hamilton et al.   NATURE

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

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

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

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

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

Enhancer RNA profiling predicts transcription factor activity

(2018) Joseph G. Azofeifa et al.   GENOME RESEARCH

An atlas of chromatin accessibility in the adult human brain

(2018) John F. Fullard et al.   GENOME RESEARCH

PM20D1 is a quantitative trait locus associated with Alzheimer’s disease

(2018) Jose V. Sanchez-Mut et al.   NATURE MEDICINE

Different Neuronal Activity Patterns Induce Different Gene Expression Programs

(2018) Kelsey M. Tyssowski et al.   NEURON

The Epigenetic State of PRDM16-Regulated Enhancers in Radial Glia Controls Cortical Neuron Position

(2018) José-Manuel Baizabal et al.   NEURON

Chromatin Regulation of Neuronal Maturation and Plasticity

(2018) David A. Gallegos et al.   TRENDS IN NEUROSCIENCES

Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease

(2018) Xianjun Dong et al.   NATURE NEUROSCIENCE

RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation

(2018) Homa Rahnamoun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers

(2016) Rui Lopes et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2016) S. John Liu et al.   SCIENCE

Extra-coding RNAs regulate neuronal DNA methylation dynamics

(2016) Katherine E. Savell et al.   Nature Communications

Brain enhancer activities at the gene-poor 5p14.1 autism-associated locus

(2016) Yukiko U. Inoue et al.   Scientific Reports

Functional Characterization of Schizophrenia-Associated Variation in CACNA1C

(2016) Nicole Eckart et al.   PLoS One

ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells

(2016) Christopher D. Scharer et al.   Scientific Reports

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS

(2015) J. M. Gray et al.   JOURNAL OF NEUROSCIENCE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

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

(2015) Nicola A Kearns et al.   NATURE METHODS

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner 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

Coexpression networks identify brain region–specific enhancer RNAs in the human brain

(2015) Pu Yao et al.   NATURE NEUROSCIENCE

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum

(2015) Christopher L Frank et al.   NATURE NEUROSCIENCE

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

(2015)   NATURE NEUROSCIENCE

Stimulus-specific combinatorial functionality of neuronal c-fos enhancers

(2015) Jae-Yeol Joo et al.   NATURE NEUROSCIENCE

LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation

(2015) Francesca Telese et al.   NEURON

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers

(2015) Sarah Voisin et al.   Genome Medicine

Restless Legs Syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon

(2014) D. Spieler et al.   GENOME RESEARCH

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

Histone H2A.Z subunit exchange controls consolidation of recent and remote memory

(2014) Iva B. Zovkic et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

(2014) Athar N Malik et al.   NATURE NEUROSCIENCE

Transcriptional Regulation of Enhancers Active in Protodomains of the Developing Cerebral Cortex

(2014) Kartik Pattabiraman et al.   NEURON

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

(2014) C.-L. Hsieh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for Noncoding Variation in Schizophrenia

(2014) Panos Roussos et al.   Cell Reports

Large-Scale Identification of Coregulated Enhancer Networks in the Adult Human Brain

(2014) Marit W. Vermunt et al.   Cell Reports

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

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

(2013) Alex S. Nord et al.   CELL

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Enhancer mutations and phenotype modularity

(2013) Christopher T Gordon et al.   NATURE GENETICS

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

DNA methylation regulates associative reward learning

(2013) Jeremy J Day et al.   NATURE NEUROSCIENCE

The LIM homeobox gene Isl1 is required for the correct development of the striatonigral pathway in the mouse

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

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cultured Subventricular Zone Progenitor Cells Transduced with Neurogenin-2 Become Mature Glutamatergic Neurons and Integrate into the Dentate Gyrus

(2012) Xia Chen et al.   PLoS One

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Differential Activity by Polymorphic Variants of a Remote Enhancer that Supports Galanin Expression in the Hypothalamus and Amygdala: Implications for Obesity, Depression and Alcoholism

(2011) Scott Davidson et al.   NEUROPSYCHOPHARMACOLOGY

Genome-wide association study of comorbid depressive syndrome and alcohol dependence

(2011) Alexis C. Edwards et al.   PSYCHIATRIC GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Neurogenin 2 has an essential role in development of the dentate gyrus

(2008) C. Galichet et al.   DEVELOPMENT

Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein

(2008) Yongsu Jeong et al.   NATURE GENETICS

SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons

(2008) K. Y. Kwan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY