The PAF1 complex promotes 3′ processing of pervasive transcripts

Integrator is a genome-wide attenuator of non-productive transcription

(2021) Søren Lykke-Andersen et al.   MOLECULAR CELL

Structural basis of Integrator-mediated transcription regulation

(2021) Isaac Fianu et al.   SCIENCE

CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG

(2020) Zhihui Liu et al.   Nature Communications

CDK13 cooperates with CDK12 to control global RNA polymerase II processivity

(2020) Zheng Fan et al.   Science Advances

Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

(2020) Seychelle M. Vos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

(2020) Michael Tellier et al.   NUCLEIC ACIDS RESEARCH

The Integrator Complex in Transcription and Development

(2020) María Saraí Mendoza-Figueroa et al.   TRENDS IN BIOCHEMICAL SCIENCES

Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation

(2020) Lu Lv et al.   eLife

Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase

(2020) Hai Zheng et al.   SCIENCE

Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control

(2019) Lee Davidson et al.   Cell Reports

Paf1C regulates RNA polymerase II progression by modulating elongation rate

(2019) Liming Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation

(2019) Laura Godfrey et al.   Nature Communications

The Integrator complex cleaves nascent mRNAs to attenuate transcription

(2019) Deirdre C. Tatomer et al.   GENES & DEVELOPMENT

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

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

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes

(2019) Nathan D. Elrod et al.   MOLECULAR CELL

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

(2018) Yong Zhu et al.   MOLECULAR CELL

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

(2018) Anthony C. Chiu et al.   MOLECULAR CELL

Controlling nuclear RNA levels

(2018) Manfred Schmid et al.   NATURE REVIEWS GENETICS

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

(2018) Lovorka Stojic et al.   NUCLEIC ACIDS RESEARCH

Integrator subunit 4 is a ‘Symplekin-like’ scaffold that associates with INTS9/11 to form the Integrator cleavage module

(2018) Todd R Albrecht et al.   NUCLEIC ACIDS RESEARCH

Emerging Roles of Non-Coding RNA Transcription

(2018) Minna U. Kaikkonen et al.   TRENDS IN BIOCHEMICAL SCIENCES

Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila

(2018) Zaijun Ma et al.   eLife

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

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

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

Global transcriptional activity dynamics reveal functional enhancer RNAs

(2018) Yoon Jung Kim et al.   GENOME RESEARCH

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors

(2017) John C. Zinder et al.   GENES & DEVELOPMENT

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation

(2017) Margaux Michel et al.   Molecular Systems Biology

Molecular basis for the interaction between Integrator subunits IntS9 and IntS11 and its functional importance

(2017) Yixuan Wu 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

Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation

(2017) S. Branden Van Oss et al.   TRENDS IN BIOCHEMICAL SCIENCES

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

(2017) Benedikt Zacher et al.   PLoS One

TGF-β Tumor Suppression through a Lethal EMT

(2016) Charles J. David et al.   CELL

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts

(2016) Nicola Meola et al.   MOLECULAR CELL

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors

(2016) Tinghu Zhang et al.   Nature Chemical Biology

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

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation

(2016) Yan Yang et al.   PLoS Genetics

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

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

(2015) Fei Xavier Chen et al.   CELL

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

(2015) Evangelos Pefanis et al.   CELL

The Integrator complex controls the termination of transcription at diverse classes of gene targets

(2015) Jeffrey R Skaar et al.   CELL RESEARCH

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

(2015) Yongsheng Shi et al.   GENES & DEVELOPMENT

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

(2015) Qing-Fu Cao et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II

(2015) M. Yu et al.   SCIENCE

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Integrator: surprisingly diverse functions in gene expression

(2015) David Baillat et al.   TRENDS IN BIOCHEMICAL SCIENCES

Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing

(2014) Dirk Heckl et al.   NATURE BIOTECHNOLOGY

Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

(2014) Bernd Stadelmayer et al.   Nature Communications

DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes

(2014) Junichi Yamamoto et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Characterization of molecular and cellular functions of the cyclin-dependent kinase CDK9 using a novel specific inhibitor

(2013) T K Albert et al.   BRITISH JOURNAL OF PHARMACOLOGY

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

SET1 and p300 Act Synergistically, through Coupled Histone Modifications, in Transcriptional Activation by p53

(2013) Zhanyun Tang et al.   CELL

The human cap-binding complex is functionally connected to the nuclear RNA exosome

(2013) Peter Refsing Andersen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

(2011) Pascal Preker et al.   NUCLEIC ACIDS RESEARCH

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

(2011) R. A. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Paf1 complex: Platform or player in RNA polymerase II transcription?

(2010) Judith A. Jaehning   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Human PAF1 Complex Acts in Chromatin Transcription Elongation Both Independently and Cooperatively with SII/TFIIS

(2010) Jaehoon Kim 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

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A Genome-Scale RNAi Screen for Oct4 Modulators Defines a Role of the Paf1 Complex for Embryonic Stem Cell Identity

(2009) Li Ding et al.   Cell Stem Cell

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors

(2009) Orit Rozenblatt-Rosen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY