Transcription imparts architecture, function and logic to enhancer units

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

(2019) Molly Gasperini et al.   CELL

The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptads

(2019) Feiyue Lu et al.   MOLECULAR CELL

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

In vivo profiling of metastatic double knockouts through CRISPR–Cpf1 screens

(2019) Ryan D. Chow et al.   NATURE METHODS

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing

(2019) Wanqing Shao et al.   eLife

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

(2018) Nathaniel D. Tippens et al.   GENES & DEVELOPMENT

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques 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

Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells

(2018) Hong Sook Kim et al.   NATURE

Positional specificity of different transcription factor classes within enhancers

(2018) Sharon R. Grossman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers

(2018) Jacob M. Tome et al.   NATURE GENETICS

The punctilious RNA polymerase II core promoter

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

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

(2017) Julia Joung et al.   NATURE

Is a super-enhancer greater than the sum of its parts?

(2017) Noah Dukler et al.   NATURE GENETICS

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

(2017) Felix Muerdter et al.   NATURE METHODS

RTFBSDB: an integrated framework for transcription factor binding site analysis

(2016) Zhong Wang et al.   BIOINFORMATICS

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis

(2016) Jialiang Huang et al.   DEVELOPMENTAL CELL

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

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

(2016) Jesse M. Engreitz et al.   NATURE

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

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

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

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

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

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

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

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations

(2014) Xiaomu Wei et al.   PLoS Genetics

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

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

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

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