RNA polymerase II pausing in development: orchestrating transcription

Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation

(2021) Daniel C.L. Robinson et al.   DEVELOPMENTAL CELL

SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape

(2021) Shibin Hu et al.   MOLECULAR CELL

SPT5 stabilization of promoter-proximal RNA polymerase II

(2021) Yuki Aoi et al.   MOLECULAR CELL

What Is a Transcriptional Burst?

(2020) Edward Tunnacliffe et al.   TRENDS IN GENETICS

TFIID Enables RNA Polymerase II Promoter-Proximal Pausing

(2020) Charli B. Fant et al.   MOLECULAR CELL

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

(2020) Yuki Aoi et al.   MOLECULAR CELL

Release of promoter–proximal paused Pol II in response to histone deacetylase inhibition

(2020) Roshan Vaid et al.   NUCLEIC ACIDS RESEARCH

Negative elongation factor complex enables macrophage inflammatory responses by controlling anti-inflammatory gene expression

(2020) Li Yu et al.   Nature Communications

Live Visualization of ERK Activity in the Mouse Blastocyst Reveals Lineage-Specific Signaling Dynamics

(2020) Claire S. Simon et al.   DEVELOPMENTAL CELL

Cell-Cycle-Dependent ERK Signaling Dynamics Direct Fate Specification in the Mammalian Preimplantation Embryo

(2020) Michael J. Pokrass et al.   DEVELOPMENTAL CELL

Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency

(2019) Tüzer Kalkan et al.   Cell Stem Cell

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

(2019) Pengyi Yang et al.   Cell Systems

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing

(2019) Jean-Pierre Etchegaray et al.   MOLECULAR CELL

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

An efficient auxin-inducible degron system with low basal degradation in human cells

(2019) Shiqian Li et al.   NATURE METHODS

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

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

Dynamic lineage priming is driven via direct enhancer regulation by ERK

(2019) William B. Hamilton et al.   NATURE

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

(2018) Melanie A. Eckersley-Maslin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II

(2018) Barbara Steurer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transient pausing by RNA polymerase II

(2018) David H. Price   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages

(2018) Maria A Sacta et al.   eLife

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning

(2018) Sophie M Morgani et al.   eLife

Symmetry Breaking in the Mammalian Embryo

(2018) Hui Ting Zhang et al.   Annual Review of Cell and Developmental Biology

Dynamic turnover of paused Pol II complexes at human promoters

(2018) Benjamin Erickson et al.   GENES & DEVELOPMENT

Emerging Principles of Gene Expression Programs and Their Regulation

(2018) Scott D. Pope et al.   MOLECULAR CELL

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

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

(2018) Caroline R. Bartman et al.   MOLECULAR CELL

Genomic encoding of transcriptional burst kinetics

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

RNA polymerase II pausing and transcriptional regulation of the HSP70 expression

(2017) Heeyoun Bunch   EUROPEAN JOURNAL OF CELL BIOLOGY

Acetylation on histone H3 lysine 9 mediates a switch from transcription initiation to elongation

(2017) Leah A. Gates et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters

(2017) Arnaud R. Krebs et al.   MOLECULAR CELL

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription pausing regulates mouse embryonic stem cell differentiation

(2017) Melodi Tastemel et al.   Stem Cell Research

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Symmetry breaking in development and stochastic gene expression

(2017) Jonathan R. Chubb   Wiley Interdisciplinary Reviews-Developmental Biology

NODAL Secures Pluripotency upon Embryonic Stem Cell Progression from the Ground State

(2017) Carla Mulas et al.   Stem Cell Reports

RNA polymerase II pausing modulates hematopoietic stem cell emergence in zebrafish

(2016) Q. Yang et al.   BLOOD

Negative feedback regulation of the ERK1/2 MAPK pathway

(2016) David Lake et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Lineage specification in the mouse preimplantation embryo

(2016) Claire Chazaud et al.   DEVELOPMENT

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

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide

(2015) Fei Chen et al.   GENES & DEVELOPMENT

Pausing of RNA Polymerase II Regulates Mammalian Developmental Potential through Control of Signaling Networks

(2015) Lucy H. Williams et al.   MOLECULAR CELL

RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition

(2015) Ann Samarakkody et al.   NUCLEIC ACIDS RESEARCH

Translational Initiation at a Non-AUG Start Codon for Human and Mouse Negative Elongation Factor-B

(2015) Haihui Pan et al.   PLoS One

Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways

(2015) Xiuli Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

Cell signaling and transcription factors regulating cell fate during formation of the mouse blastocyst

(2015) Tristan Frum et al.   TRENDS IN GENETICS

Endogenous WNT Signals Mediate BMP-Induced and Spontaneous Differentiation of Epiblast Stem Cells and Human Embryonic Stem Cells

(2015) Dorota Kurek et al.   Stem Cell Reports

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Klf2 Is an Essential Factor that Sustains Ground State Pluripotency

(2014) Jia-Chi Yeo et al.   Cell Stem Cell

RNA polymerase II pausing during development

(2014) B. Gaertner et al.   DEVELOPMENT

Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation

(2014) M. S. Buckley et al.   GENES & DEVELOPMENT

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos

(2014) D. M. Messerschmidt et al.   GENES & DEVELOPMENT

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

(2014) Heeyoun Bunch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activin/Nodal signalling before implantation: setting the stage for embryo patterning

(2014) C. Papanayotou et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ERK1 phosphorylates Nanog to regulate protein stability and stem cell self-renewal

(2014) Sung-Hyun Kim et al.   Stem Cell Research

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

(2014) Iris Jonkers et al.   eLife

Control of Transcriptional Elongation

(2013) Hojoong Kwak et al.   Annual Review of Genetics

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha et al.   CELL

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

(2013) A. Saunders et al.   GENES & DEVELOPMENT

Anatomy of a blastocyst: Cell behaviors driving cell fate choice and morphogenesis in the early mouse embryo

(2013) Nadine Schrode et al.   GENESIS

BRD4 Coordinates Recruitment of Pause Release Factor P-TEFb and the Pausing Complex NELF/DSIF To Regulate Transcription Elongation of Interferon-Stimulated Genes

(2013) M. C. Patel et al.   MOLECULAR AND CELLULAR BIOLOGY

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

The Elongation Complex Components BRD4 and MLLT3/AF9 Are Transcriptional Coactivators of Nuclear Retinoid Receptors

(2013) Sébastien Flajollet et al.   PLoS One

Epiblast Ground State Is Controlled by Canonical Wnt/β-Catenin Signaling in the Postimplantation Mouse Embryo and Epiblast Stem Cells

(2013) Tomoyuki Sumi et al.   PLoS One

Modulation of β-catenin function maintains mouse epiblast stem cell and human embryonic stem cell self-renewal

(2013) Hoon Kim et al.   Nature Communications

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

(2013) Kai Chen et al.   eLife

The Spt4–Spt5 complex: A multi-faceted regulator of transcription elongation

(2012) Grant A. Hartzog et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Mediator complex and transcription elongation

(2012) Ronald C. Conaway et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

(2012) Graziano Martello et al.   Cell Stem Cell

FGF4 is required for lineage restriction and salt-and-pepper distribution of primitive endoderm factors but not their initial expression in the mouse

(2012) M. Kang et al.   DEVELOPMENT

Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks

(2012) D. A. Gilchrist et al.   GENES & DEVELOPMENT

Control of ground-state pluripotency by allelic regulation of Nanog

(2012) Yusuke Miyanari et al.   NATURE

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Estrogen receptor-α recruits P-TEFb to overcome transcriptional pausing in intron 1 of the MYB gene

(2012) Partha Mitra et al.   NUCLEIC ACIDS RESEARCH

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Signaling Mechanisms Controlling Cell Fate and Embryonic Patterning

(2012) N. Perrimon et al.   Cold Spring Harbor Perspectives in Biology

Defining the Status of RNA Polymerase at Promoters

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

Activated STAT1 Transcription Factors Conduct Distinct Saltatory Movements in the Cell Nucleus

(2011) Jasmin Speil et al.   BIOPHYSICAL JOURNAL

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide

(2011) S. S. Teves et al.   GENES & DEVELOPMENT

Genetic and Genomic Analyses of RNA Polymerase II-pausing Factor in Regulation of Mammalian Transcription and Cell Growth

(2011) Jianlong Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Negative Elongation Factor Accelerates the Rate at Which Heat Shock Genes Are Shut off by Facilitating Dissociation of Heat Shock Factor

(2011) S. K. B. Ghosh et al.   MOLECULAR AND CELLULAR BIOLOGY

Opposing effects of Tcf3 and Tcf1 control Wnt stimulation of embryonic stem cell self-renewal

(2011) Fei Yi et al.   NATURE CELL BIOLOGY

Inhibition of glycogen synthase kinase-3 alleviates Tcf3 repression of the pluripotency network and increases embryonic stem cell resistance to differentiation

(2011) Jason Wray et al.   NATURE CELL BIOLOGY

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Stochastic Mechanisms of Cell Fate Specification that Yield Random or Robust Outcomes

(2010) Robert J. Johnston et al.   Annual Review of Cell and Developmental Biology

Dual specificity phosphatase 6 (DUSP6) is an ETS-regulated negative feedback mediator of oncogenic ERK signaling in lung cancer cells

(2010) Zhenfeng Zhang et al.   CARCINOGENESIS

TIF1γ Controls Erythroid Cell Fate by Regulating Transcription Elongation

(2010) Xiaoying Bai et al.   CELL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

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

(2010) Daniel A. Gilchrist et al.   CELL

NELF Potentiates Gene Transcription in the Drosophila Embryo

(2010) Xiaoling Wang et al.   PLoS One

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Suppression of Erk signalling promotes ground state pluripotency in the mouse embryo

(2009) J. Nichols et al.   DEVELOPMENT

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mouse Cofactor of BRCA1 (Cobra1) Is Required for Early Embryogenesis

(2009) Asma Amleh et al.   PLoS One

Differentiation of Embryonic Stem Cells to Clinically Relevant Populations: Lessons from Embryonic Development

(2008) Charles E. Murry et al.   CELL

Molecular Regulation of H3K4 Trimethylation by Wdr82, a Component of Human Set1/COMPASS

(2008) M. Wu et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2008) Leighton J. Core et al.   SCIENCE