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Getting up to speed with transcription elongation by RNA polymerase II

1 of 135 checkable references need attention · checked 2026-08-29

At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.

References needing attention

marked retracted — notice via Crossref, record curated by Retraction Watch10.1038/nature12535

Genomic organization of human transcription initiation complexes

The 134 checked references that resolve

resolves10.1146/annurev-genet-110711-155440

Control of Transcriptional Elongation

resolves10.1038/nrg3293

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

resolves10.1126/science.1229386

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

resolves10.1038/emboj.2013.111

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

resolves10.1016/j.molcel.2014.02.014

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

resolves10.1016/j.molcel.2006.06.014

Controlling the Elongation Phase of Transcription with P-TEFb

resolves10.1146/annurev-biochem-052610-095910

RNA Polymerase II Elongation Control

resolves10.1101/gad.14.7.792

P-TEFb kinase recruitment and function at heat shock loci

resolves10.7554/eLife.02407

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

resolves10.1016/j.molcel.2013.02.015

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

resolves10.1016/j.molcel.2010.11.005

Splicing-Dependent RNA Polymerase Pausing in Yeast

resolves10.1101/gr.171405.113

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

resolves10.1186/gb-2014-15-5-r69

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

resolves10.1016/j.cell.2014.03.048

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

resolves10.1016/j.molcel.2014.03.044

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

resolves10.1038/emboj.2013.167

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

resolves10.1016/j.molcel.2003.08.001

A Slow RNA Polymerase II Affects Alternative Splicing In Vivo

resolves10.4161/rna.28646

Adventures in time and space

resolves10.1128/MCB.25.8.3276-3285.2005

Strong Polyadenylation and Weak Pausing Combine To Cause Efficient Termination of Transcription in the Human Gγ-Globin Gene

resolves10.1128/MCB.26.10.3986-3996.2006

Pause Sites Promote Transcriptional Termination of Mammalian RNA Polymerase II

resolves10.1038/nature13787

R-loops induce repressive chromatin marks over mammalian gene terminators

resolves10.1016/j.molcel.2012.10.014

Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination

resolves10.1038/nrm3952

Structural basis of transcription initiation by RNA polymerase II

resolves10.1038/nrm3943

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

resolves10.1038/nrm3941

Histone exchange, chromatin structure and the regulation of transcription

resolves10.1016/j.cell.2013.07.032

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

resolves10.1016/j.celrep.2012.08.034

Defining the Status of RNA Polymerase at Promoters

resolves10.1016/j.cell.2010.03.030

c-Myc Regulates Transcriptional Pause Release

resolves10.1016/j.molcel.2013.10.001

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

resolves10.1126/science.1162228

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

resolves10.1101/gad.2005511

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

resolves10.1126/science.1181421

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

resolves10.1016/j.cell.2010.10.004

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

resolves10.1101/gad.6.2.284

DNA sequence requirements for generating paused polymerase at the start of hsp70.

resolves10.1101/gad.9.22.2756

HSF access to heat shock elements in vivo depends critically on promoter architecture defined by GAGA factor, TFIID, and RNA polymerase II binding sites.

resolves10.1016/j.cell.2013.04.033

Global Regulation of Promoter Melting in Naive Lymphocytes

resolves10.1126/science.1068356

Coordination of PIC Assembly and Chromatin Remodeling During Differentiation-Induced Gene Activation

resolves10.1016/j.molcel.2012.03.006

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

resolves10.1016/j.cell.2012.08.004

Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII

resolves10.1016/j.molcel.2011.10.022

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

resolves10.1016/j.molcel.2011.12.014

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

resolves10.1074/jbc.M113.544395

Functional Interactions of the RNA Polymerase II-interacting Proteins Gdown1 and TFIIF

resolves10.1101/gad.246173.114

Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide

resolves10.1101/gad.231886.113

Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation

resolves10.1101/gad.215459.113

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

resolves10.1016/S0092-8674(88)91087-2

The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged

resolves10.1016/j.cell.2007.05.042

A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells

resolves10.1038/ng.2007.26

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

resolves10.1016/j.cell.2013.04.045

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

resolves10.1126/science.1131399

Initial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism

resolves10.1016/j.molcel.2005.05.024

The Role of the Transcription Bubble and TFIIB in Promoter Clearance by RNA Polymerase II

resolves10.1093/nar/gku147

Regulation of promoter-proximal transcription elongation: enhanced DNA scrunching drives λQ antiterminator-dependent escape from a σ70-dependent pause

resolves10.1073/pnas.0802406105

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

resolves10.1038/ng.3142

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

resolves10.1016/j.molcel.2013.05.016

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

resolves10.1016/j.cell.2009.05.047

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

resolves10.1038/nrm3949

The selection and function of cell type-specific enhancers

resolves10.1038/nrm3951

The Mediator complex: a central integrator of transcription

resolves10.1016/j.cell.2011.06.005

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

resolves10.1038/nature13417

Enhancer loops appear stable during development and are associated with paused polymerase

resolves10.1128/MCB.02224-07

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

resolves10.1016/S0378-1119(00)00240-7

Chromatin organization and transcriptional control of gene expression in Drosophila

resolves10.1016/j.ydbio.2008.02.008

Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3

resolves10.1128/MCB.16.5.2044

Three Functional Classes of Transcriptional Activation Domains

resolves10.1101/gad.9.5.559

Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation.

resolves10.1038/nsmb.2878

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

resolves10.1371/journal.pone.0072289

Polo-Like Kinase 1 Inhibits the Activity of Positive Transcription Elongation Factor of RNA Pol II b (P-TEFb)

resolves10.1101/gad.2015411

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

resolves10.1093/nar/gku449

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation

resolves10.1016/j.molcel.2005.06.027

The Bromodomain Protein Brd4 Is a Positive Regulatory Component of P-TEFb and Stimulates RNA Polymerase II-Dependent Transcription

resolves10.1038/onc.2013.179

Brd4 maintains constitutively active NF-κB in cancer cells by binding to acetylated RelA

resolves10.1128/MCB.01365-08

Brd4 Coactivates Transcriptional Activation of NF-κB via Specific Binding to Acetylated RelA

resolves10.1128/MCB.00182-12

The Super Elongation Complex Family of RNA Polymerase II Elongation Factors: Gene Target Specificity and Transcriptional Output

resolves10.1101/gad.2059211

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

resolves10.1016/j.molcel.2011.12.008

The Little Elongation Complex Regulates Small Nuclear RNA Transcription

resolves10.1016/j.molcel.2010.01.026

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

resolves10.1038/nrm3417

The super elongation complex (SEC) family in transcriptional control

resolves10.1016/j.molcel.2014.08.004

Integrator Regulates Transcriptional Initiation and Pause Release following Activation

resolves10.1016/j.cell.2009.12.050

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

resolves10.1073/pnas.1314754110

Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin

resolves10.1073/pnas.1107107108

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

resolves10.1371/journal.pone.0064880

The Elongation Complex Components BRD4 and MLLT3/AF9 Are Transcriptional Coactivators of Nuclear Retinoid Receptors

resolves10.1016/j.bbagrm.2013.04.007

Transcriptional Control by NF-κB: Elongation in Focus

resolves10.1128/MCB.01152-07

RelA Ser 276 Phosphorylation Is Required for Activation of a Subset of NF-κB-Dependent Genes by Recruiting Cyclin-Dependent Kinase 9/Cyclin T1 Complexes

resolves10.1016/S1097-2765(01)00314-8

NF-κB Binds P-TEFb to Stimulate Transcriptional Elongation by RNA Polymerase II

resolves10.1073/pnas.1108190108

Targeting MYC dependence in cancer by inhibiting BET bromodomains

resolves10.1016/j.cell.2013.03.036

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

resolves10.1016/j.cell.2011.08.017

BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc

resolves10.1038/ni.2065

Crosstalk in NF-κB signaling pathways

resolves10.1093/nar/gku529

ATM regulates NF-κB-dependent immediate-early genes via RelA Ser 276 phosphorylation coupled to CDK9 promoter recruitment

resolves10.1016/j.celrep.2013.11.003

Transcription Factors Mediate the Enzymatic Disassembly of Promoter-Bound 7SK snRNP to Locally Recruit P-TEFb for Transcription Elongation

resolves10.1101/gad.187781.112

Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks

resolves10.1016/j.cell.2013.04.028

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

resolves10.1073/pnas.0903188106

7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development

resolves10.1016/j.cell.2013.09.053

Super-Enhancers in the Control of Cell Identity and Disease

resolves10.1016/j.cell.2013.03.035

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

resolves10.1016/j.molcel.2014.08.024

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

resolves10.1038/nature11884

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

resolves10.1128/MCB.22.9.2918-2927.2002

Evidence that Negative Elongation Factor Represses Transcription Elongation through Binding to a DRB Sensitivity-Inducing Factor/RNA Polymerase II Complex and RNA

resolves10.1016/j.molcel.2014.08.023

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

resolves10.1371/journal.pgen.1003382

Genome-Wide Control of RNA Polymerase II Activity by Cohesin

resolves10.1016/0092-8674(90)90218-4

Spatial and temporal patterns of E74 transcription during Drosophila development

resolves10.1016/j.bbagrm.2012.08.013

Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription

resolves10.1038/nsmb1352

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

resolves10.1016/j.celrep.2013.08.013

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

resolves10.1038/nsmb.2470

Regulation of nucleosome dynamics by histone modifications

resolves10.1016/j.cell.2012.10.009

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

resolves10.1038/emboj.2009.56

Spt6 enhances the elongation rate of RNA polymerase II in vivo

resolves10.1016/j.molcel.2014.04.013

H2B Ubiquitylation Promotes RNA Pol II Processivity via PAF1 and pTEFb

resolves10.1101/gr.120634.111

H2B monoubiquitylation is a 5′-enriched active transcription mark and correlates with exon–intron structure in human cells

resolves10.1146/annurev.biochem.72.121801.161551

The RNA Polymerase II Elongation Complex

resolves10.1016/j.celrep.2012.03.013

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

resolves10.1038/nsmb.1658

Nucleosome positioning as a determinant of exon recognition

resolves10.1038/nsmb.1659

Chromatin organization marks exon-intron structure

resolves10.1038/nature10925

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

resolves10.1038/nsmb.1924

Reciprocal intronic and exonic histone modification regions in humans

resolves10.1038/nsmb.1995

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

resolves10.1073/pnas.0810666106

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

resolves10.1101/gr.111070.110

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

resolves10.1038/nsmb.2867

RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement

resolves10.1016/j.molcel.2011.04.026

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

resolves10.1038/mtna.2014.34

New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization

resolves10.1016/j.cell.2013.02.014

Transcriptional Regulation and Its Misregulation in Disease

resolves10.1038/nature10334

RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia

resolves10.1038/nature10509

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia

resolves10.1038/nsmb.1666

Rates of in situ transcription and splicing in large human genes

resolves10.1038/nature09652

Nascent transcript sequencing visualizes transcription at nucleotide resolution

resolves10.1038/nature05025

Dynamics of heat shock factor association with native gene loci in living cells

resolves10.1083/jcb.200706018

The transcriptional cycle of HIV-1 in real-time and live cells

resolves10.1371/journal.pbio.1000573

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

resolves10.1038/nsmb1280

In vivo dynamics of RNA polymerase II transcription

resolves10.1038/ng0295-184

The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced

resolves10.1016/j.molcel.2005.02.017

Distinction and Relationship between Elongation Rate and Processivity of RNA Polymerase II In Vivo

resolves10.1038/nsmb.2143

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

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