Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers

Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity

(2019) Laura L. Colbran et al.   GENETICS

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

(2018) Tahsin Stefan Barakat et al.   Cell Stem Cell

Enhancer transcription: what, where, when, and why?

(2018) Nathaniel D. Tippens 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

Eukaryotic core promoters and the functional basis of transcription initiation

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

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

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

(2018) Xinchen Wang et al.   Nature Communications

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

(2017) Felix Muerdter et al.   NATURE METHODS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

FANTOM5 CAGE profiles of human and mouse samples

(2017) Shuhei Noguchi et al.   Scientific Data

Enhancer-derived RNA: A Primer

(2017) Feng Liu   GENOMICS PROTEOMICS & BIOINFORMATICS

Unlinking an lncRNA from Its Associated cis Element

(2016) Vikram R. Paralkar et al.   MOLECULAR CELL

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

(2016) René Dreos et al.   NUCLEIC ACIDS RESEARCH

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

(2016) René Dreos et al.   PLoS Computational Biology

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks

(2015) Peter Hansen et al.   GENOME RESEARCH

STARR-seq — Principles and applications

(2015) Felix Muerdter et al.   GENOMICS

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model

(2014) Robin Andersson   BIOESSAYS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson 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

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

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

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Structural visualization of key steps in human transcription initiation

(2013) Yuan He et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

(2013) Leila Taher et al.   GENOME BIOLOGY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

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

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

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

(2011) R. A. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perspectives on the RNA polymerase II core promoter

(2011) James T. Kadonaga   Wiley Interdisciplinary Reviews-Developmental Biology

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

(2010) T. J. Parry et al.   GENES & DEVELOPMENT

Sequence features that drive human promoter function and tissue specificity

(2010) J. M. Landolin et al.   GENOME RESEARCH

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

The basal initiation machinery: beyond the general transcription factors

(2009) Timothy W. Sikorski et al.   CURRENT OPINION IN CELL BIOLOGY

Enhancers: The abundance and function of regulatory sequences beyond promoters

(2009) Michael Bulger et al.   DEVELOPMENTAL BIOLOGY

CpG islands - ‘A rough guide’

(2009) Robert S. Illingworth et al.   FEBS LETTERS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Characterization of sINR, a strict version of the Initiator core promoter element

(2009) Ganit Yarden et al.   NUCLEIC ACIDS RESEARCH

The RNA polymerase II core promoter — the gateway to transcription

(2008) Tamar Juven-Gershon et al.   CURRENT OPINION IN CELL BIOLOGY

Caudal, a key developmental regulator, is a DPE-specific transcriptional factor

(2008) T. Juven-Gershon et al.   GENES & DEVELOPMENT

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE