A 50 year history of technologies that drove discovery in eukaryotic transcription regulation

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

(2019) Molly Gasperini et al.   CELL

Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation

(2019) Stephen L. McDaniel et al.   MOLECULAR CELL

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms

(2019) Robert G. Roeder   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Pioneer transcription factors shape the epigenetic landscape

(2018) Alexandre Mayran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Imaging of native transcription factors and histone phosphorylation at high resolution in live cells

(2018) Sascha Conic et al.   JOURNAL OF CELL BIOLOGY

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Structure of human TFIID and mechanism of TBP loading onto promoter DNA

(2018) Avinash B. Patel et al.   SCIENCE

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

(2017) Anniina Vihervaara et al.   Nature Communications

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

(2017) Fedor Kouzine et al.   Cell Systems

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation

(2016) Fabiana M. Duarte et al.   GENES & DEVELOPMENT

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation

(2016) Dig B. Mahat et al.   MOLECULAR CELL

Genomic Organization of Human Transcription Initiation Complexes

(2016) B. Franklin Pugh et al.   PLoS One

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

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

(2014) Leighton J Core et al.   NATURE GENETICS

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Global Regulation of Promoter Melting in Naive Lymphocytes

(2013) Fedor Kouzine et al.   CELL

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

(2013) Jian Li et al.   MOLECULAR CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

(2013) William S Kruesi et al.   eLife

Defining the Status of RNA Polymerase at Promoters

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

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Recruitment Timing and Dynamics of Transcription Factors at the Hsp70 Loci in Living Cells

(2010) Katie L. Zobeck et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

RNA polymerase II–TFIIB structure and mechanism of transcription initiation

(2009) Dirk Kostrewa et al.   NATURE

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger et al.   SCIENCE

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

(2009) S. Nechaev et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE