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

The origins of developmental gene regulation

(2017) César Arenas-Mena   EVOLUTION & DEVELOPMENT

The punctilious RNA polymerase II core promoter

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

Promoter shape varies across populations and affects promoter evolution and expression noise

(2017) Ignacio E Schor et al.   NATURE GENETICS

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao 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

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen 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

Genetic variants regulating expression levels and isoform diversity during embryogenesis

(2016) Enrico Cannavò et al.   NATURE

Genome-wide mapping of autonomous promoter activity in human cells

(2016) Joris van Arensbergen et al.   NATURE BIOTECHNOLOGY

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

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

Human Promoters Are Intrinsically Directional

(2015) Sascha H.C. Duttke et al.   MOLECULAR CELL

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

Core promoters in transcription: old problem, new insights

(2015) Ananda L. Roy et al.   TRENDS IN BIOCHEMICAL SCIENCES

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

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

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon 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

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

(2014) Robin Andersson et al.   Nature Communications

Uncovering Enhancer Functions Using the α-Globin Locus

(2014) Douglas Vernimmen   PLoS Genetics

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

(2014) Han Wu et al.   PLoS Genetics

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

(2014) Xiao-Yong Li et al.   eLife

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

(2013) R. A.- J. Chen et al.   GENOME RESEARCH

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

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

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

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

(2013) C. D. Arnold et al.   SCIENCE

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

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

(2012) Guillaume Junion et al.   CELL

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

(2012) Guoliang Li et al.   CELL

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

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

(2012) Stefan Bonn et al.   NATURE GENETICS

Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

(2012) Stefan Bonn et al.   Nature Protocols

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Discovery of active enhancers through bidirectional expression of short transcripts

(2011) Michael F Melgar et al.   GENOME BIOLOGY

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE