RNA Polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation

Pol II Docking and Pausing at Growth and Stress Genes in C. elegans

(2014) Colin S. Maxwell et al.   Cell Reports

Control of Transcriptional Elongation

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

Taking a Pause to Reflect on Morphogenesis

(2013) Abbie Saunders et al.   CELL

Transitions for Regulating Early Transcription

(2013) Margaux Michel et al.   CELL

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code

(2013) Célia Jeronimo et al.   CHEMICAL REVIEWS

NusG-Spt5 Proteins—Universal Tools for Transcription Modification and Communication

(2013) Sushil Kumar Tomar et al.   CHEMICAL REVIEWS

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

RNA Polymerase II Transcription Elongation Control

(2013) Jiannan Guo et al.   CHEMICAL REVIEWS

Phosphorylation of RNA polymerase II is independent of P-TEFb in the C. elegans germline

(2013) E. A. Bowman et al.   DEVELOPMENT

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

In vivo live imaging of RNA polymerase II transcription factories in primary cells

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

To Grow or Not to Grow: Nutritional Control of Development During Caenorhabditis elegans L1 Arrest

(2013) L. R. Baugh   GENETICS

The transcription start site landscape of C. elegans

(2013) T. L. Saito et al.   GENOME RESEARCH

The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

(2013) R. A.- J. Chen et al.   GENOME RESEARCH

Cap Completion and C-Terminal Repeat Domain Kinase Recruitment Underlie the Initiation-Elongation Transition of RNA Polymerase II

(2013) M. Lidschreiber et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2013) Jian Li et al.   MOLECULAR CELL

The ZFP-1(AF10)/DOT-1 Complex Opposes H2B Ubiquitination to Reduce Pol II Transcription

(2013) Germano Cecere et al.   MOLECULAR CELL

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

(2013) Telmo Henriques et al.   MOLECULAR CELL

Structural visualization of key steps in human transcription initiation

(2013) Yuan He et al.   NATURE

Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex

(2013) K. Murakami et al.   SCIENCE

Emerging roles for RNA polymerase II CTD in Arabidopsis

(2013) Mohsen Hajheidari et al.   TRENDS IN PLANT SCIENCE

Lost in Transcription: Molecular Mechanisms that Control HIV Latency

(2013) Ran Taube et al.   Viruses-Basel

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

(2013) William S Kruesi et al.   eLife

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription

(2012) Martin Heidemann et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

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

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation

(2012) Corinna Hintermair et al.   EMBO JOURNAL

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

(2012) F. A. Steiner et al.   GENOME RESEARCH

Cross-talk Among RNA Polymerase II Kinases Modulates C-terminal Domain Phosphorylation

(2012) Ballachanda N. Devaiah et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cyclin K-containing Kinase Complexes Maintain Self-renewal in Murine Embryonic Stem Cells

(2012) Qian Dai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Nexus for Gene Expression—Molecular Mechanisms of Spt5 and NusG in the Three Domains of Life

(2012) Finn Werner   JOURNAL OF MOLECULAR BIOLOGY

The Yeast Cap Binding Complex Modulates Transcription Factor Recruitment and Establishes Proper Histone H3K36 Trimethylation during Active Transcription

(2012) M. A. Hossain et al.   MOLECULAR AND CELLULAR BIOLOGY

A Universal RNA Polymerase II CTD Cycle Is Orchestrated by Complex Interplays between Kinase, Phosphatase, and Isomerase Enzymes along Genes

(2012) Alain R. Bataille et al.   MOLECULAR CELL

Transcriptional Regulation by Pol II(G) Involving Mediator and Competitive Interactions of Gdown1 and TFIIF with Pol II

(2012) Miki Jishage et al.   MOLECULAR CELL

Functional Association of Gdown1 with RNA Polymerase II Poised on Human Genes

(2012) Bo Cheng et al.   MOLECULAR CELL

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

(2012) Ho Sung Rhee et al.   NATURE

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

The super elongation complex (SEC) family in transcriptional control

(2012) Zhuojuan Luo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II

(2012) Stéphane Larochelle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BRD4 is an atypical kinase that phosphorylates Serine2 of the RNA Polymerase II carboxy-terminal domain

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

CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II

(2012) A. Mayer et al.   SCIENCE

Defining the Status of RNA Polymerase at Promoters

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

A Positive Feedback Loop Links Opposing Functions of P-TEFb/Cdk9 and Histone H2B Ubiquitylation to Regulate Transcript Elongation in Fission Yeast

(2012) Miriam Sansó et al.   PLoS Genetics

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

(2011) Jun Odawara et al.   BMC GENOMICS

Human Mediator Subunit MED26 Functions as a Docking Site for Transcription Elongation Factors

(2011) Hidehisa Takahashi et al.   CELL

Clamping the clamp of RNA polymerase

(2011) Vladimir Svetlov et al.   EMBO JOURNAL

Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity

(2011) Fuensanta W Martinez-Rucobo et al.   EMBO JOURNAL

An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression

(2011) R. R. Pferdehirt et al.   GENES & DEVELOPMENT

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

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

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

(2011) D. Blazek et al.   GENES & DEVELOPMENT

Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC)

(2011) C. Lin et al.   GENES & DEVELOPMENT

The super elongation complex (SEC) and MLL in development and disease

(2011) E. Smith et al.   GENES & DEVELOPMENT

Regulation of Fertility, Survival, and Cuticle Collagen Function by theCaenorhabditis elegans eaf-1andell-1Genes

(2011) Liquan Cai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Competing for the Clamp: Promoting RNA Polymerase Processivity and Managing the Transition from Initiation to Elongation

(2011) Grant A. Hartzog et al.   MOLECULAR CELL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Function of leukemogenic mixed lineage leukemia 1 (MLL) fusion proteins through distinct partner protein complexes

(2011) D. Biswas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Polymerase-Associated Factor complex (PAFc) connects the Super Elongation Complex (SEC) to RNA polymerase II on chromatin

(2011) N. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription

(2011) B. Matija Peterlin et al.   Wiley Interdisciplinary Reviews-RNA

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

(2011) Brian T Wilhelm et al.   GENOME BIOLOGY

A Higher-Order Complex Containing AF4 and ENL Family Proteins with P-TEFb Facilitates Oncogenic and Physiologic MLL-Dependent Transcription

(2010) Akihiko Yokoyama et al.   CANCER CELL

Activation-Induced Cytidine Deaminase Targets DNA at Sites of RNA Polymerase II Stalling by Interaction with Spt5

(2010) Rushad Pavri 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

A Gene-Specific Requirement of RNA Polymerase II CTD Phosphorylation for Sexual Differentiation in S. pombe

(2010) Damien Coudreuse et al.   CURRENT BIOLOGY

CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1

(2010) B. Bartkowiak et al.   GENES & DEVELOPMENT

A global analysis of C. elegans trans-splicing

(2010) M. A. Allen et al.   GENOME RESEARCH

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

RNA Polymerase II C-Terminal Domain Phosphorylation Patterns in Caenorhabditis elegans Operons, Polycistronic Gene Clusters with Only One Promoter

(2010) A. Garrido-Lecca et al.   MOLECULAR AND CELLULAR BIOLOGY

Separable Functions of the Fission Yeast Spt5 Carboxyl-Terminal Domain (CTD) in Capping Enzyme Binding and Transcription Elongation Overlap with Those of the RNA Polymerase II CTD

(2010) S. Schneider et al.   MOLECULAR AND CELLULAR BIOLOGY

AFF4, a Component of the ELL/P-TEFb Elongation Complex and a Shared Subunit of MLL Chimeras, Can Link Transcription Elongation to Leukemia

(2010) Chengqi Lin et al.   MOLECULAR CELL

HIV-1 Tat Assembles a Multifunctional Transcription Elongation Complex and Stably Associates with the 7SK snRNP

(2010) Bijan Sobhian et al.   MOLECULAR CELL

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

Gene-specific RNA polymerase II phosphorylation and the CTD code

(2010) Hyunmin Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chemical-genomic dissection of the CTD code

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

CDK8 is a positive regulator of transcriptional elongation within the serum response network

(2010) Aaron J Donner 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

The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors

(2010) Alfonso Rodríguez-Gil et al.   NUCLEIC ACIDS RESEARCH

Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif

(2010) Angela Hirtreiter et al.   NUCLEIC ACIDS RESEARCH

RNA polymerase and transcription elongation factor Spt4/5 complex structure

(2010) B. J. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex

(2010) A. Missra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of transcription start sites of trans-spliced genes: Uncovering unusual operon arrangements

(2010) J. J. Morton et al.   RNA

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Trans-generational epigenetic regulation of C. elegans primordial germ cells

(2010) Hirofumi Furuhashi et al.   Epigenetics & Chromatin

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

(2010) Mei Zhong et al.   PLoS Genetics

RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast

(2010) Tae Soo Kim et al.   GENOME BIOLOGY

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

Cellular dynamics of the negative transcription elongation factor NELF

(2009) Tetsu M.C. Yung et al.   EXPERIMENTAL CELL RESEARCH

TFIIH-Associated Cdk7 Kinase Functions in Phosphorylation of C-Terminal Domain Ser7 Residues, Promoter-Proximal Pausing, and Termination by RNA Polymerase II

(2009) K. Glover-Cutter et al.   MOLECULAR AND CELLULAR BIOLOGY

Phosphorylation of the Transcription Elongation Factor Spt5 by Yeast Bur1 Kinase Stimulates Recruitment of the PAF Complex

(2009) Y. Liu et al.   MOLECULAR AND CELLULAR BIOLOGY

Phosphorylation of the Pol II CTD by KIN28 Enhances BUR1/BUR2 Recruitment and Ser2 CTD Phosphorylation Near Promoters

(2009) Hongfang Qiu et al.   MOLECULAR CELL

TFIIH and P-TEFb Coordinate Transcription with Capping Enzyme Recruitment at Specific Genes in Fission Yeast

(2009) Laia Viladevall et al.   MOLECULAR CELL

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

(2009) K. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest

(2009) L. Ryan Baugh 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

Misguided Transcriptional Elongation Causes Mixed Lineage Leukemia

(2009) Dorothee Mueller et al.   PLOS BIOLOGY

The transition from transcriptional initiation to elongation

(2008) Joseph T Wade et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

(2008) C. Lee 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

Cracking the RNA polymerase II CTD code

(2008) Sylvain Egloff et al.   TRENDS IN GENETICS