Topic 119

polymerase transcription rna elongation pol ii promoter dna transcriptional rnap molecular pausing binding complex initiation terminal factor termination domain rnapii promoters pause template yeast proximal ctd cerevisiae biochemistry recruitment processivity productive regulation paused synthesis saccharomyces nascent subunit transcribed mrna chromatin interaction site dependent upstream sites catalytic polymerases conserved subunits coupled factors complexes mechanism interacts stall biology protein does translesion bound nucleosomes stalled genes start loop general its bind cryo rnas release nusg vivo pic gene essential binds carboxy interact coupling holoenzyme sigma elongating exit cyclin active nucleotides eukaryotes pre at show nuclear through processive directly not histone sequence recruited tss

90 items. Top items listed below.

Spt5 phosphorylation and the Rtf1 Plus3 domain promote Rtf1 function through distinct mechanisms 119 102 49 31 3

A general role of zinc binding domain revealed by structures of σ28-dependent transcribing complexes 119 51 31 8 3

O-GlcNAc Transferase Activity is Essential for RNA Pol II Pausing in a Human Cell-Free Transcription System 119 31 3

Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling 119 31 3

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair 119 46 31 3

Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1 119 49 31 3

The INO80 remodeler couples premature termination of mRNA synthesis with transcription elongation 119 31 3

Anti-pausing activity of region 4 of the RNA polymerase σ subunit and its regulation by σ-remodeling factors 119 31 3

PAF1 facilitates RNA polymerase II ubiquitination by the Elongin A complex through phosphorylation by CDK12 119 34 3

Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation 119 31 8 3

The nucleosome DNA entry-exit site is important for transcription termination in Saccharomyces cerevisiae 119 31 9 3

Structure of the TFIIIC subcomplex {tau} A provides insights into RNA polymerase III pre-initiation complex formation 119 31 8 3

Mechanism of upstream promoter element stimulation of transcription at a ribosomal RNA promoter determined by single-molecule imaging 119 8 3

The cryo-electron microscopy structure of the human CDK-activating kinase 119 51 8 3

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II 119 102 31 3

Altered Mediator dynamics during heat shock in budding yeast 119 31 3

Integrator terminates promoter-proximal Pol II to generate C. elegans piRNA precursors 119 31 3

Promoter-specific changes in initiation, elongation and homeostasis of histone H3 acetylation during CBP/p300 Inhibition 119 31 3

Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription 119 8 3

Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function 119 31 8

BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation 119 46 31 3

m6A RNA methylation regulates promoter proximal pausing of RNA Polymerase II 119 31 3

Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction 119 31 3

Structural basis of ribosomal RNA transcription regulation 119 51 8 3

Escherichia coli NusG links the lead ribosome with the transcription elongation complex 119 51 8 3

Human Prefoldin Modulates Co-transcriptional Pre-mRNA Splicing 119 49 34 31 3

The γ-herpesviral TATA box binding protein directly interacts with RNA Polymerase II to direct late gene transcription 119 41 31 8 3

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner 119 31 8 3

Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs 119 49 31 3

Structural basis for the activation of CDK7 by MAT1 and Cyclin H 119 63 8 3

Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription 119 31 3

Auto-inhibitory regulation of DNA binding by the C-terminal tails of the mitochondrial transcription factors Mtf1 and TFB2M 119 8 3

PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC 119 49 31 3

Integrator is a genome-wide attenuator of non-productive transcription 119 31 3

TATA and paused promoters active in differentiated tissues have distinct expression characteristics 31 9

Transcriptional down-regulation of metabolic genes by Gdown1 ablation induces quiescent cell re-entry into the cell cycle 119 3

The impediment to replication at tRNA genes in S. cerevisiae does not require tRNA transcription, and is facilitated by topoisomerases and Rad18-dependent repair pathways 119 46 31 3

A dual role for H2A.Z.1 in modulating the dynamics of RNA Polymerase II initiation and elongation 119 31 20 3

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase 119 51 8 3

Identification of novel RNA Polymerase II CTD interaction sites on the mRNA Capping Enzyme 119 8 3

An interaction between Gβγ and RNA polymerase II regulates transcription in cardiac fibroblasts 119 102 3

Promoter-proximal elongation regulates transcription in archaea 119 31 3

AraC mutations that suppress inactivating mutations in the C-terminal domain of the RpoA subunit of Escherichia coli RNA polymerase 119 31 3

Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Associates with RNA Polymerase II Pausing 31 20 3

Fusion protein EWS-FLI1 is incorporated into a protein granule in cells 119 78 8 3

The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription in Saccharomyces cerevisiae 119 31 3

Mediator complex subunit Med19 binds directly GATA DNA-binding zinc finger and functions with Med1 in GATA-driven gene regulation in vivo 119 31 3

Assembly of a double-stranded RNA synthesizing complex: RNA-DEPENDENT RNA POLYMERASE 2 docks with NUCLEAR RNA POLYMERASE IV at the clamp domain 119 49 31 8 3

Structure of the Mammalian Mediator 51 8 3

Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration 119 31 9

Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene 119 31 18 8

Rapid and Efficient Co-Transcriptional Splicing Enhances Mammalian Gene Expression 119 49 31 9 3

Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the "shooting gallery" 119 31

Defining a critical enhancer near Nanog using chromatin-focused approaches identifies RNA Pol II recruitment as required for expression 31 9

Selective metal ion utilization contributes to the transformation of the activity of yeast polymerase η from DNA polymerization toward RNA polymerization 119 46 3

Transcription coordinates histone amounts and genome content 119 31 3

RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding 119 91 8

Architectural Mediator subunits are differentially essential for global transcription in yeast 119 3

Structure of a transcribing RNA polymerase II-U1 snRNP complex 119 51 49 8 3

RNA sequence and structure determinants of Pol III transcriptional termination in human cells 119 49 31

The origin and evolution of a distinct mechanism of transcription initiation in yeasts 119 49 31 9

TBPL2/TFIIA complex overhauls oocyte transcriptome during oocyte growth 119 31 20 3

Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting 119 31 3

NusG is an intrinsic transcription termination factor that stimulates motility and coordinates global gene expression with NusA 119 49 31 3

The histone variant macroH2A1.1 regulates gene expression by direct association with their transcription start site. 31 9 3

Chemical transcription roadblocking for nascent RNA display 119 46 8

Neuronal Activity-Induced BRG1 Phosphorylation Regulates Enhancer Activation 31 3

ASXL1 Directs Neutrophilic Differentiation via Modulation of MYC and RNA Polymerase II. 93 31 9 3

Structural characterization of an RNA bound antiterminator protein reveal a successive binding mode 119 8 3

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency 93 31 20 3

The RNA Polymerase II core subunit RPB-9 directs transcriptional elongation at piRNA loci in Caenorhabditis elegans 90 49 31 20 3

CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites 119 31

A unique arginine cluster in PolDIP2 enhances nucleotide binding and DNA synthesis by PrimPol 119 46 8 3

Residence Time Analysis of RNA Polymerase Transcription Dynamics: A Bayesian Sticky HMM Approach 119 38 4

Nuclear myosin VI regulates the spatial organization of mammalian transcription initiation. 31 20 3

Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast 49 31 9 3

Histone modifications at the transcription start site of non-coding RNA revealed regulatory patterns of activation in Caenorhabditis elegans embryo 31 9 3

The Drosophila HP1 family is associated with active gene expression across chromatin contexts 31 9 3

RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates 119 31 3

RanBP2-mediated SUMOylation promotes human DNA polymerase lambda nuclear localization and DNA repair 119 46 34 3

The histone methyltransferase SETD2 couples transcription and splicing by engaging pre-mRNA processing factors through its SHI domain 49 31 3

Structural basis of transcription-translation coupling and collision in bacteria. 119 49 8 3

Alteration of the premature tRNA landscape by gammaherpesvirus infection 49 41 31 9 3

Kinetic-Mechanistic Evidence for Which E. coli RNA Polymerase-{lambda}PR Open Promoter Complex Initiates and for Stepwise Disruption of Contacts in Bubble Collapse 119 8

Chromatin-associated MRN complex protects highly transcribing genes from genomic instability 31 9 3

Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase 119 51 8

Histone lysine crotonylation regulates cell-fate determination of neural stem/progenitor cells by activating bivalent promoters 93 31 20 3

Bacterial promoter opening underpins ubiquitous transcriptional regulation by DNA supercoiling 119 31

A PP2A-Integrator complex fine-tunes transcription by opposing CDK9 119 102 31 3

Biophysical and dynamic characterization of a fine-tuned binding of the human Respiratory Syncytial Virus M2-1 core domain to long RNAs 119 8

Regulation of SETD2 stability is important for the fidelity of H3K36me3 deposition 119 49 46 3

In-cell architecture of an actively transcribing-translating expressome 119 51 8 3

Identification of PCNA interacting protein motifs in human DNA polymerase delta 119 63 8 3

Structural basis of transcription-translation coupling 136 51 49 8 3

Escherichia coli σ38 promoters use two UP elements instead of a -35 element: resolution of a paradoxand discovery that σ38 transcribes ribosomal promoters 119

Transcriptional regulation of ACSL1 by CHREBP and NF-kappa B in macrophages during hyperglycemia and inflammation 150 110 49 3

Bypass of DNA Interstrand crosslinks by a Rev1-DNA polymerase ζ complex 119 46 8

Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements 31 9 3

A dynamic regulatory interface on SARS-CoV-2 RNA polymerase 44 1

Heterotrimeric PCNA Increases the Activity and Fidelity of Dbh, a Y-family Translesion DNA Polymerase Prone to Creating Single-Base Deletion Mutations 119 63 8