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Control of RNA Polymerase II Promoter-Proximal Pausing by DNA Supercoiling

https://doi.org/10.1101/2020.05.12.091058

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Production and Titration of Lentiviral Vectors

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Underwinding of DNA on Binding of Yeast TFIID to the TATA Element

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Isopeptide bond in collagen- and fibrinogen-binding MSCRAMMs

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DNA supercoiling during transcription

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Effects of DNA supercoiling on chromatin architecture

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DNA topology and a minimal set of basal factors for transcription by RNA polymerase II

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Transcription elongation factors DSIF and NELF: Promoter-proximal pausing and beyond

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

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ATM-Dependent Chromatin Changes Silence Transcription In cis to DNA Double-Strand Breaks

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Mechanism of Transcriptional Bursting in Bacteria

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Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

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

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RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

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Genome Organization Drives Chromosome Fragility

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Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

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Defining the Status of RNA Polymerase at Promoters

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Bon voyage: A transcriptional journey around DNA breaks

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Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC)

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Promoter proximal pausing and the control of gene expression

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Gene regulation in the immediate-early response process

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Enhancer RNA Facilitates NELF Release from Immediate Early Genes

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Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity

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Spatial Chromosome Folding and Active Transcription Drive DNA Fragility and Formation of Oncogenic MLL Translocations

inferredcites →https://doi.org/10.1016/j.molcel.2020.02.014openalex-snapshot

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

inferredcites →https://doi.org/10.1016/j.mrfmmm.2012.07.005openalex-snapshot

The DNA topoisomerase II catalytic inhibitor merbarone is genotoxic and induces endoreduplication

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Immediate early response genes and cell transformation

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Negative elongation factor NELF controls transcription of immediate early genes in a stimulus-specific manner

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Stimulation of 3T3 cells induces transcription of the c-fos proto-oncogene

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DNA topoisomerase IIα is required for RNA polymerase II transcription on chromatin templates

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Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes

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High‐resolution profiling of γH2AX around DNA double strand breaks in the mammalian genome

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BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo

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A high-resolution map of active promoters in the human genome

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BAF complexes facilitate decatenation of DNA by topoisomerase IIα

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Topoisomerases facilitate transcription of long genes linked to autism

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Transcriptional elongation requires DNA break-induced signalling

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Gene regulation and priming by topoisomerase IIα in embryonic stem cells

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ATM specifically mediates repair of double-strand breaks with blocked DNA ends

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Paused RNA polymerase II inhibits new transcriptional initiation

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Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements

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ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

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

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Roles of eukaryotic topoisomerases in transcription, replication and genomic stability

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Transcription-coupled DNA repair: two decades of progress and surprises

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The functional response of upstream DNA to dynamic supercoiling in vivo

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DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks

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Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

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Transcription-dependent dynamic supercoiling is a short-range genomic force

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Transcription-generated torsional stress destabilizes nucleosomes

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The dynamic response of upstream DNA to transcription-generated torsional stress

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Negative supercoil at gene boundaries modulates gene topology

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Target genes of Topoisomerase IIβ regulate neuronal survival and are defined by their chromatin state

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DNA supercoiling allows enhancer action over a large distance

inferredcites →https://doi.org/10.1073/pnas.84.20.7024openalex-snapshot

Supercoiling of the DNA template during transcription.

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Merbarone Inhibits the Catalytic Activity of Human Topoisomerase IIα by Blocking DNA Cleavage

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Topoisomerase II is required for the production of long Pol II gene transcripts in yeast

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Easy quantitative assessment of genome editing by sequence trace decomposition

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A positioned +1 nucleosome enhances promoter-proximal pausing

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Are TADs supercoiled?

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

inferredcites →https://doi.org/10.1101/gad.325142.119openalex-snapshot

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

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A Topoisomerase IIß-Mediated dsDNA Break Required for Regulated Transcription

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

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

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Transcription Under Torsion

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ZATT (ZNF451)–mediated resolution of topoisomerase 2 DNA-protein cross-links

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Role of Topoisomerase IIβ in the Expression of Developmentally Regulated Genes

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Transcription as a Threat to Genome Integrity

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Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types

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Visualization of unconstrained negative supercoils of DNA on polytene chromosomes ofDrosophila

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DNA Topoisomerases Maintain Promoters in a State Competent for Transcriptional Activation in Saccharomyces cerevisiae

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TDP2–Dependent Non-Homologous End-Joining Protects against Topoisomerase II–Induced DNA Breaks and Genome Instability in Cells and In Vivo

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TOP2B: The First Thirty Years

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DNA topology and transcription

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Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity

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Author response: Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4776521openalex-extracted

Gene Co-Expression Networks Describe the Catalytic Inhibition of DNA Topoisomerase Iigene

inferred← citeshttps://doi.org/10.1016/j.celrep.2020.108569openalex-snapshot

DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks

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