4.8 Article

RNA-Mediated Feedback Control of Transcriptional Condensates

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Formation of Multiphase Complex Coacervates and Partitioning of Biomolecules within them

Gregory A. Mountain et al.

BIOMACROMOLECULES (2020)

Review Biochemistry & Molecular Biology

Molecular structure in biomolecular condensates

Ivan Peran et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

Letter Biotechnology & Applied Microbiology

The nf-core framework for community-curated bioinformatics pipelines

Philip A. Ewels et al.

NATURE BIOTECHNOLOGY (2020)

Review Genetics & Heredity

What Is a Transcriptional Burst?

Edward Tunnacliffe et al.

TRENDS IN GENETICS (2020)

Review Biochemistry & Molecular Biology

Transcription in Living Cells: Molecular Mechanisms of Bursting

Joseph Rodriguez et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 89 (2020)

Article Multidisciplinary Sciences

MeCP2 links heterochromatin condensates and neurodevelopmental disease

Charles H. Li et al.

NATURE (2020)

Article Multidisciplinary Sciences

Partitioning of cancer therapeutics in nuclear condensates

Isaac A. Klein et al.

SCIENCE (2020)

Review Biochemistry & Molecular Biology

Biomolecular Condensates in the Nucleus

Benjamin R. Sabari et al.

TRENDS IN BIOCHEMICAL SCIENCES (2020)

Article Biochemistry & Molecular Biology

Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

Sreejith J. Nair et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Review Cell Biology

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

Leighton Core et al.

GENES & DEVELOPMENT (2019)

Article Multidisciplinary Sciences

Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties

Steven Boeynaems et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Enhancer Features that Drive Formation of Transcriptional Condensates

Krishna Shrinivas et al.

MOLECULAR CELL (2019)

Article Biochemistry & Molecular Biology

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

Alicia V. Zamudio et al.

MOLECULAR CELL (2019)

Review Multidisciplinary Sciences

Organization and regulation of gene transcription

Patrick Cramer

NATURE (2019)

Review Biochemistry & Molecular Biology

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

Robert G. Roeder

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Cell Biology

The liquid nucleome - phase transitions in the nucleus at a glance

Amy R. Strom et al.

JOURNAL OF CELL SCIENCE (2019)

Article Multidisciplinary Sciences

LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells

Gary LeRoy et al.

SCIENCE ADVANCES (2019)

Article Multidisciplinary Sciences

Genomic encoding of transcriptional burst kinetics

Anton J. M. Larsson et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Reentrant Phase Transitions and Non-Equilibrium Dynamics in Membraneless Organelles

Anthony N. Milin et al.

BIOCHEMISTRY (2018)

Article Cell Biology

Widespread transcriptional pausing and elongation control at enhancers

Telmo Henriques et al.

GENES & DEVELOPMENT (2018)

Article Biochemistry & Molecular Biology

Enhancer RNA profiling predicts transcription factor activity

Joseph G. Azofeifa et al.

GENOME RESEARCH (2018)

Article Chemistry, Physical

Polyelectrolyte complex coacervation by electrostatic dipolar interactions

Sabin Adhikari et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

Review Biochemistry & Molecular Biology

The Role of RNA in Biological Phase Separations

Marta M. Fay et al.

JOURNAL OF MOLECULAR BIOLOGY (2018)

Article Polymer Science

Salt Partitioning in Complex Coacervation of Symmetric Polyelectrolytes

Pengfei Zhang et al.

MACROMOLECULES (2018)

Article Multidisciplinary Sciences

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

Barbara Steurer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

RNA buffers the phase separation behavior of prion-like RNA binding proteins

Shovamayee Maharana et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

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

Benjamin R. Sabari et al.

SCIENCE (2018)

Article Genetics & Heredity

Functional classification of long non-coding RNAs by k-mer content

Jessime M. Kirk et al.

NATURE GENETICS (2018)

Article Biochemistry & Molecular Biology

RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation

Homa Rahnamoun et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Multidisciplinary Sciences

Compartmentalised RNA catalysis in membrane-free coacervate protocells

Bjoern Drobot et al.

NATURE COMMUNICATIONS (2018)

Article Chemistry, Physical

Theory of polyelectrolyte complexation-Complex coacervates are self-coacervates

Kris T. Delaney et al.

JOURNAL OF CHEMICAL PHYSICS (2017)

Letter Biotechnology & Applied Microbiology

Nextflow enables reproducible computational workflows

Paolo Di Tommaso et al.

NATURE BIOTECHNOLOGY (2017)

Review Cell Biology

Biomolecular condensates: organizers of cellular biochemistry

Salman F. Banani et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Review Multidisciplinary Sciences

Liquid phase condensation in cell physiology and disease

Yongdae Shin et al.

SCIENCE (2017)

Article Chemistry, Physical

Development of the modern theory of polymeric complex coacervation

Charles E. Sing

ADVANCES IN COLLOID AND INTERFACE SCIENCE (2017)

Article Chemistry, Multidisciplinary

Reentrant Phase Transition Drives Dynamic Substructure Formation in Ribonucleoprotein Droplets

Priya R. Banerjee et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

Article Biochemistry & Molecular Biology

The Ground State and Evolution of Promoter Region Directionality

Yi Jin et al.

Review Biochemistry & Molecular Biology

A Phase Separation Model for Transcriptional Control

Denes Hnisz et al.

Article Biochemistry & Molecular Biology

Enhancer Control of Transcriptional Bursting

Takashi Fukaya et al.

Review Cell Biology

What have single-molecule studies taught us about gene expression?

Huimin Chen et al.

GENES & DEVELOPMENT (2016)

Article Chemistry, Multidisciplinary

Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg2+, Nucleotides, and RNA

Erica A. Frankel et al.

LANGMUIR (2016)

Review Genetics & Heredity

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

Wenbo Li et al.

NATURE REVIEWS GENETICS (2016)

Article Polymer Science

Electrostatic correlations in polyelectrolyte solutions

M. Muthukumar

POLYMER SCIENCE SERIES A (2016)

Article Chemistry, Multidisciplinary

Systematic study of the dynamics and half-lives of newly synthesized proteins in human cells

Weixuan Chen et al.

CHEMICAL SCIENCE (2016)

Article Biochemistry & Molecular Biology

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

Evangelos Pefanis et al.

Article Biochemistry & Molecular Biology

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

Benjamin S. Scruggs et al.

MOLECULAR CELL (2015)

Article Biochemistry & Molecular Biology

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

Timothy J. Nott et al.

MOLECULAR CELL (2015)

Article Multidisciplinary Sciences

Transcription factor trapping by RNA in gene regulatory elements

Alla A. Sigova et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

The many faces of long noncoding RNAs

Alessandro Gardini et al.

FEBS JOURNAL (2015)

Review Biochemistry & Molecular Biology

Building Robust Transcriptomes with Master Splicing Factors

Mohini Jangi et al.

Article Biochemistry & Molecular Biology

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

Katie Schaukowitch et al.

MOLECULAR CELL (2014)

Article Multidisciplinary Sciences

An atlas of active enhancers across human cell types and tissues

Robin Andersson et al.

NATURE (2014)

Article Biochemistry & Molecular Biology

RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template

Dave A. Pai et al.

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Warren A. Whyte et al.

Article Multidisciplinary Sciences

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

Ibrahim I. Cisse et al.

SCIENCE (2013)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Genetics & Heredity

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

Karen Adelman et al.

NATURE REVIEWS GENETICS (2012)

Article Biochemistry & Molecular Biology

Fast transcription rates of RNA polymerase II in human cells

Paolo Maiuri et al.

EMBO REPORTS (2011)

Article Biochemical Research Methods

Systems-wide Proteomic Analysis in Mammalian Cells Reveals Conserved, Functional Protein Turnover

Sidney B. Cambridge et al.

JOURNAL OF PROTEOME RESEARCH (2011)

Article Biochemistry & Molecular Biology

The Sequence Read Archive

Rasko Leinonen et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

David M. Suter et al.

SCIENCE (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Widespread transcription at neuronal activity-regulated enhancers

Tae-Kyung Kim et al.

NATURE (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Computer Science, Interdisciplinary Applications

FiPy: Partial Differential Equations with Python

Jonathan E. Guyer et al.

COMPUTING IN SCIENCE & ENGINEERING (2009)

Article Biochemistry & Molecular Biology

Rates of in situ transcription and splicing in large human genes

Jarnail Singh et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Biotechnology & Applied Microbiology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead et al.

GENOME BIOLOGY (2009)

Review Biochemistry & Molecular Biology

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Arjun Raj et al.

Article Biochemistry & Molecular Biology

The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription

Gary LeRoy et al.

MOLECULAR CELL (2008)

Review Multidisciplinary Sciences

Feedback loops shape cellular signals in space and time

Onn Brandman et al.

SCIENCE (2008)

Article Multidisciplinary Sciences

Divergent Transcription from Active Promoters

Amy C. Seila et al.

SCIENCE (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Transcriptional noise and the fidelity of initiation by RNA polymerase II

Kevin Struhl

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Stochastic mRNA synthesis in mammalian cells

Arjun Raj et al.

PLOS BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Transcriptional pulsing of a developmental gene

JR Chubb et al.

CURRENT BIOLOGY (2006)

Article Genetics & Heredity

Dynamics of the p53-Mdm2 feedback loop in individual cells

G Lahav et al.

NATURE GENETICS (2004)

Article Biochemistry & Molecular Biology

The UCSC Table Browser data retrieval tool

D Karolchik et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Modulation of transcription factor function by an amino acid: activation of Put3p by proline

CA Sellick et al.

EMBO JOURNAL (2003)

Article Multidisciplinary Sciences

A synthetic oscillatory network of transcriptional regulators

MB Elowitz et al.

NATURE (2000)

Article Multidisciplinary Sciences

Construction of a genetic toggle switch in Escherichia coli

TS Gardner et al.

NATURE (2000)