Genome-wide uniformity of human ‘open’ pre-initiation complexes

Structure of transcribing mammalian RNA polymerase II

(2016) Carrie Bernecky et al.   NATURE

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly

(2016) Robert K. Louder et al.   NATURE

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Perspectives on Unidirectional versus Divergent Transcription

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

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble

(2015) Christopher O. Barnes et al.   MOLECULAR CELL

Human Gene Promoters Are Intrinsically Bidirectional

(2015) Robin Andersson et al.   MOLECULAR CELL

Human Promoters Are Intrinsically Directional

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

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Robin Andersson   BIOESSAYS

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

(2014) Ho Sung Rhee et al.   CELL

A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription

(2014) Sebastian Marquardt et al.   CELL

TFIIH Phosphorylation of the Pol II CTD Stimulates Mediator Dissociation from the Preinitiation Complex and Promoter Escape

(2014) Koon Ho Wong et al.   MOLECULAR CELL

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle 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

Kin28 regulates the transient association of Mediator with core promoters

(2014) Célia Jeronimo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcribing through the nucleosome

(2014) Sheila S. Teves et al.   TRENDS IN BIOCHEMICAL SCIENCES

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

(2014) Mathieu Quinodoz et al.   GENOME BIOLOGY

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing

(2013) Jian Li et al.   MOLECULAR CELL

Structural visualization of key steps in human transcription initiation

(2013) Yuan He et al.   NATURE

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

(2013) Tianyin Zhou et al.   NUCLEIC ACIDS RESEARCH

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

(2013) H. Kwak et al.   SCIENCE

ArchTEx: accurate extraction and visualization of next-generation sequence data

(2012) William K. M. Lai et al.   BIOINFORMATICS

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

(2012) Sarah Sainsbury et al.   NATURE

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Defining the Status of RNA Polymerase at Promoters

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

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

CpG islands and the regulation of transcription

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

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

(2011) Jason Ernst et al.   NATURE

Transcription factor TFIIF is not required for initiation by RNA polymerase II, but it is essential to stabilize transcription factor TFIIB in early elongation complexes

(2011) P. Cabart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

(2011) Elizabeth A. Rach et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

RNA polymerase II–TFIIB structure and mechanism of transcription initiation

(2009) Dirk Kostrewa et al.   NATURE

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

GeneTrack--a genomic data processing and visualization framework

(2008) I. Albert et al.   BIOINFORMATICS

The RNA polymerase II core promoter — the gateway to transcription

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

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE