It’s a DoG-eat-DoG world—altered transcriptional mechanisms drive downstream-of-gene (DoG) transcript production

Heat shock induces premature transcript termination and reconfigures the human transcriptome

(2022) Simona Cugusi et al.   MOLECULAR CELL

Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression

(2021) Nicolle A. Rosa-Mercado et al.   MOLECULAR CELL

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans

(2021) Roberta Dollinger et al.   JOURNAL OF MOLECULAR BIOLOGY

CDK9 keeps RNA polymerase II on track

(2021) Sylvain Egloff   CELLULAR AND MOLECULAR LIFE SCIENCES

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

(2021) Shibin Hu et al.   MOLECULAR CELL

A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination

(2021) Mirjam Arnold et al.   MOLECULAR CELL

SPT5 stabilization of promoter-proximal RNA polymerase II

(2021) Yuki Aoi et al.   MOLECULAR CELL

Who let the DoGs out? – biogenesis of stress-induced readthrough transcripts

(2021) Nicolle A. Rosa-Mercado et al.   TRENDS IN BIOCHEMICAL SCIENCES

Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species

(2021) Natalia Petrenko et al.   eLife

Integrator enforces the fidelity of transcriptional termination at protein-coding genes

(2021) Lucas Ferreira Dasilva et al.   Science Advances

Antisense-Mediated Transcript Knockdown Triggers Premature Transcription Termination

(2020) Jong-Sun Lee et al.   MOLECULAR CELL

Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination

(2020) Fan Lai et al.   MOLECULAR CELL

Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27

(2020) Xiuye Wang et al.   Nature Communications

ARTDeco: automatic readthrough transcription detection

(2020) Samuel J. Roth et al.   BMC BIOINFORMATICS

Structure and mechanism of the RNA polymerase II transcription machinery

(2020) Allison C. Schier et al.   GENES & DEVELOPMENT

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

(2020) Kaveh Daneshvar et al.   NATURE CELL BIOLOGY

Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns

(2020) Tara Alpert et al.   Cell Reports

The Integrator complex at the crossroad of coding and noncoding RNA

(2020) Nina Kirstein et al.   CURRENT OPINION IN CELL BIOLOGY

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA

(2019) Marko Melnick et al.   PLoS One

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

Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution

(2019) Daniel A. Lorenz et al.   RNA

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

(2018) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

(2018) Lydia Herzel et al.   GENOME RESEARCH

Heat shock causes a reversible increase in RNA polymerase II occupancy downstream of mRNA genes consistent with a global loss in transcriptional termination

(2018) Joseph F. Cardiello et al.   MOLECULAR AND CELLULAR BIOLOGY

Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals

(2018) Nilay Shah et al.   MOLECULAR CELL

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

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

Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription

(2018) David L.V. Bauer et al.   Cell Reports

HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes

(2018) Thomas Hennig et al.   PLoS Pathogens

DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq

(2018) Yuval Wiesel et al.   BMC GENOMICS

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

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

(2018) Homa Rahnamoun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Two distinct transcription termination modes dictated by promoters

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

BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment

(2017) Georg E. Winter et al.   MOLECULAR CELL

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

(2017) Anna Vilborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PAF1 regulation of promoter-proximal pause release via enhancer activation

(2017) Fei Xavier Chen et al.   SCIENCE

SETting the Stage for Cancer Development: SETD2 and the Consequences of Lost Methylation

(2017) Catherine C. Fahey et al.   Cold Spring Harbor Perspectives in Medicine

Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity

(2017) Michael P Meers et al.   eLife

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Readthrough transcription: How are DoGs made and what do they do?

(2016) Anna Vilborg et al.   RNA Biology

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II

(2015) Fei Xavier Chen et al.   CELL

Differentiation of mammary tumors and reduction in metastasis uponMalat1lncRNA loss

(2015) Gayatri Arun et al.   GENES & DEVELOPMENT

RNAN6-methyladenosine methylation in post-transcriptional gene expression regulation

(2015) Yanan Yue et al.   GENES & DEVELOPMENT

Poly(A) Signal-Dependent Transcription Termination Occurs through a Conformational Change Mechanism that Does Not Require Cleavage at the Poly(A) Site

(2015) Huimin Zhang 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

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread disruption of host transcription termination in HSV-1 infection

(2015) Andrzej J. Rutkowski et al.   Nature Communications

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

(2015) Ana R Grosso et al.   eLife

Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues

(2015) Jen-Hao Cheng et al.   Scientific Reports

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

3' end formation of pre-mRNA and phosphorylation of Ser2 on the RNA polymerase II CTD are reciprocally coupled in human cells

(2014) L. Davidson et al.   GENES & DEVELOPMENT

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

(2014) Serena L. Chan et al.   GENES & DEVELOPMENT

The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition

(2014) Junwei Shi et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Calcium-mediated histone modifications regulate alternative splicing in cardiomyocytes

(2014) Alok Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

RNAP II CTD tyrosine 1 performs diverse functions in vertebrate cells

(2014) Jing-Ping Hsin et al.   eLife

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

(2014) Iris Jonkers et al.   eLife

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

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins

(2013) Kathrin Leppek et al.   NUCLEIC ACIDS RESEARCH

Alternative cleavage and polyadenylation: the long and short of it

(2013) Bin Tian et al.   TRENDS IN BIOCHEMICAL SCIENCES

RNA Polymerase II Elongation Control

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

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

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

The super elongation complex (SEC) family in transcriptional control

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

CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II

(2012) A. Mayer et al.   SCIENCE

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

Pre-mRNA splicing is a determinant of histone H3K36 methylation

(2011) S. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone Methyltransferase Gene SETD2 Is a Novel Tumor Suppressor Gene in Clear Cell Renal Cell Carcinoma

(2010) Gerben Duns et al.   CANCER RESEARCH

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

The Integrator Complex Recognizes a New Double Mark on the RNA Polymerase II Carboxyl-terminal Domain

(2010) Sylvain Egloff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

(2010) Gillian L. Dalgliesh et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

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