Crosstalk of promoter and terminator during RNA polymerase II transcription cycle

RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression

(2020) Olga Calvo   CURRENT GENETICS

Functional interaction of human Ssu72 with RNA polymerase II complexes

(2019) Benjamin M. Spector et al.   PLoS One

Global Genetic Networks and the Genotype-to-Phenotype Relationship

(2019) Michael Costanzo et al.   CELL

Twenty years of Mediator complex structural studies

(2019) Alexis Verger et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Promoter Recognition: Putting TFIID on the Spot

(2019) Tanja Bhuiyan et al.   TRENDS IN CELL BIOLOGY

RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit

(2019) Paula Allepuz-Fuster et al.   NUCLEIC ACIDS RESEARCH

Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower

(2019) Delfina Gagliardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mediator, known as a coactivator, can act in transcription initiation in an activator-independent manner in vivo

(2018) Hélène Jean-Jacques et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice

(2018) Qianli Dong et al.   PLANT JOURNAL

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

The essential and multifunctional TFIIH complex

(2018) Jenna K. Rimel et al.   PROTEIN SCIENCE

Systematic analysis of complex genetic interactions

(2018) Elena Kuzmin et al.   SCIENCE

Determinants of promoter and enhancer transcription directionality in metazoans

(2018) Mahmoud M. Ibrahim et al.   Nature Communications

Two distinct transcription termination modes dictated by promoters

(2017) Takashi S. Miki et al.   GENES & DEVELOPMENT

The complex structure and function of Mediator

(2017) Thomas M. Harper et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

(2017) Carlo Baejen et al.   MOLECULAR CELL

The Mediator Complex: At the Nexus of RNA Polymerase II Transcription

(2017) Célia Jeronimo et al.   TRENDS IN CELL BIOLOGY

P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance

(2017) Raphael Loll-Krippleber et al.   Nature Communications

Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast

(2017) Nadra Al-Husini et al.   Scientific Reports

Genome-wide analysis of chromatin packing inArabidopsis thalianaat single-gene resolution

(2016) Chang Liu et al.   GENOME RESEARCH

Promoter-Terminator Gene Loops Affect Alternative 3′-End Processing in Yeast

(2016) Mónica Lamas-Maceiras et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation

(2016) Sara C. Cloutier et al.   MOLECULAR CELL

Direct Analysis of Phosphorylation Sites on the Rpb1 C-Terminal Domain of RNA Polymerase II

(2016) Hyunsuk Suh et al.   MOLECULAR CELL

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Enhancement of Transcription by a Splicing-Competent Intron Is Dependent on Promoter Directionality

(2016) Neha Agarwal et al.   PLoS Genetics

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

(2015) Yongsheng Shi et al.   GENES & DEVELOPMENT

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

ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System

(2015) Katarzyna Oktaba et al.   MOLECULAR CELL

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

Human Promoters Are Intrinsically Directional

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

Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity

(2015) Rita Gemayel et al.   MOLECULAR CELL

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Gene looping facilitates TFIIH kinase-mediated termination of transcription

(2015) Scott Medler et al.   Scientific Reports

The Ssu72 Phosphatase Mediates the RNA Polymerase II Initiation-Elongation Transition

(2014) Jesús D. Rosado-Lugo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Terminate and make a loop: regulation of transcriptional directionality

(2014) Pawel Grzechnik et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structurally conserved and functionally divergent yeast Ssu72 phosphatases

(2013) Ana M. Rodríguez-Torres et al.   FEBS LETTERS

Srb5/Med18-mediated Termination of Transcription Is Dependent on Gene Looping

(2013) Banupriya Mukundan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mediator is an intrinsic component of the basal RNA polymerase II machinery in vivo

(2013) Thierry Lacombe et al.   NUCLEIC ACIDS RESEARCH

Are gene loops the cause of transcriptional noise?

(2013) Daniel Hebenstreit   TRENDS IN GENETICS

RNA Polymerase II Mutations Conferring Defects in Poly(A) Site Cleavage and Termination in Saccharomyces cerevisiae

(2013) Charles E. Kubicek et al.   G3-Genes Genomes Genetics

A Role for CF1A 3′ End Processing Complex in Promoter-Associated Transcription

(2013) Nadra Al Husini et al.   PLoS Genetics

Correction: An Evolutionarily Conserved Synthetic Lethal Interaction Network Identifies FEN1 as a Broad-Spectrum Target for Anticancer Therapeutic Development

(2013) Derek M. van Pel et al.   PLoS Genetics

The transcription cycle in eukaryotes: From productive initiation to RNA polymerase II recycling

(2012) Jayasha Shandilya et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast

(2012) Hannah E. Mischo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA polymerase II transcription: Structure and mechanism

(2012) Xin Liu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization

(2012) Pedro Crevillén et al.   EMBO JOURNAL

Novel interactions at the essential N-terminus of poly(A) polymerase that could regulate poly(A) addition inSaccharomyces cerevisiae

(2012) Chukwudi Ezeokonkwo et al.   FEBS LETTERS

Ssu72 Phosphatase-dependent Erasure of Phospho-Ser7 Marks on the RNA Polymerase II C-terminal Domain Is Essential for Viability and Transcription Termination

(2012) David W. Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

XPG and XPF Endonucleases Trigger Chromatin Looping and DNA Demethylation for Accurate Expression of Activated Genes

(2012) Nicolas Le May et al.   MOLECULAR CELL

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

(2012) Mohan Babu et al.   NATURE

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

(2012) Ho Sung Rhee et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Looping Mediated Interaction between the Promoter and 3′ UTR Regulates Type II Collagen Expression in Chondrocytes

(2012) Arijita Jash et al.   PLoS One

Role for gene looping in intron-mediated enhancement of transcription

(2012) A. M. Moabbi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subunit architecture of general transcription factor TFIIH

(2012) B. J. Gibbons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

Reconstitution of CF IA from Overexpressed Subunits Reveals Stoichiometry and Provides Insights into Molecular Topology

(2011) James M. B. Gordon et al.   BIOCHEMISTRY

An ending is a new beginning: Transcription termination supports re-initiation

(2011) Søren Lykke-Andersen et al.   CELL CYCLE

A conserved regulatory role for antisense RNA in meiotic gene expression in yeast

(2011) Huei-Mei Chen et al.   CURRENT OPINION IN MICROBIOLOGY

Subtelomeric repetitive elements determine TERRA regulation by Rap1/Rif and Rap1/Sir complexes in yeast

(2011) Nahid Iglesias et al.   EMBO REPORTS

Genetic Analysis Implicates the Set3/Hos2 Histone Deacetylase in the Deposition and Remodeling of Nucleosomes Containing H2A.Z

(2011) M. Hang et al.   GENETICS

Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

(2011) Steven Hahn et al.   GENETICS

Evidence for a Complex of Transcription Factor IIB (TFIIB) with Poly(A) Polymerase and Cleavage Factor 1 Subunits Required for Gene Looping

(2011) Scott Medler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Novel Role for Mediator Complex Subunit Srb5/Med18 in Termination of Transcription

(2011) Banupriya Mukundan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanism of Start Site Selection by RNA Polymerase II

(2011) Shivani Goel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes

(2011) K. K. Lee et al.   Molecular Systems Biology

Unravelling the means to an end: RNA polymerase II transcription termination

(2011) Jason N. Kuehner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A pre-initiation complex at the 3′-end of genes drives antisense transcription independent of divergent sense transcription

(2011) Struan C. Murray et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation of TFIIB Links Transcription Initiation and Termination

(2010) Yuming Wang et al.   CURRENT BIOLOGY

Crosstalk between mRNA 3′ End Processing and Transcription Initiation

(2010) Christophe K. Mapendano et al.   MOLECULAR CELL

Transcriptional regulation by small RNAs at sequences downstream from 3′ gene termini

(2010) Xuan Yue et al.   Nature Chemical Biology

Chemical-genomic dissection of the CTD code

(2010) Joshua R Tietjen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Uniform transitions of the general RNA polymerase II transcription complex

(2010) Andreas Mayer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation

(2010) Stefania Millevoi et al.   NUCLEIC ACIDS RESEARCH

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Functional Organization of the S. cerevisiae Phosphorylation Network

(2009) Dorothea Fiedler et al.   CELL

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Eukaryotic transcription initiation

(2009) Shankarling Krishnamurthy et al.   CURRENT BIOLOGY

A physiological role for gene loops in yeast

(2009) Jean-Philippe Lainé et al.   GENES & DEVELOPMENT

Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex

(2009) Sue Mei Tan-Wong et al.   GENES & DEVELOPMENT

Transcription termination by nuclear RNA polymerases

(2009) P. Richard et al.   GENES & DEVELOPMENT

Gene Looping Is Conferred by Activator-dependent Interaction of Transcription Initiation and Termination Machineries

(2009) Belal El Kaderi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lymphoid Enhancer Binding Factor 1 Regulates Transcription through Gene Looping

(2009) K. Yun et al.   JOURNAL OF IMMUNOLOGY

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

Mediator complex association with constitutively transcribed genes in yeast

(2009) S. A. Ansari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation

(2009) S. Holbein et al.   RNA

Genetic interaction network of the Saccharomyces cerevisiae type 1 phosphatase Glc7

(2008) Michael R Logan et al.   BMC GENOMICS

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

A Genetic Interaction Map of RNA-Processing Factors Reveals Links between Sem1/Dss1-Containing Complexes and mRNA Export and Splicing

(2008) Gwendolyn M. Wilmes et al.   MOLECULAR CELL

Transcription-Dependent Gene Looping of the HIV-1 Provirus Is Dictated by Recognition of Pre-mRNA Processing Signals

(2008) Kelly J. Perkins et al.   MOLECULAR CELL

Cotranscriptional Recruitment of the mRNA Export Factor Yra1 by Direct Interaction with the 3′ End Processing Factor Pcf11

(2008) Sara Ann Johnson et al.   MOLECULAR CELL

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

(2008) Leighton J. Core et al.   SCIENCE