RNA Polymerase II

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  Subject Areas on Research

  • A DNA damage response system associated with the phosphoCTD of elongating RNA polymerase II. 
  • A five-gene phylogeny of Pezizomycotina. 
  • A mutation in the largest subunit of RNA polymerase II alters RNA chain elongation in vitro. 
  • A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. 
  • A positive addition to a negative tail's tale. 
  • A protein kinase that phosphorylates the C-terminal repeat domain of the largest subunit of RNA polymerase II. 
  • A transcription factor affinity-based code for mammalian transcription initiation. 
  • Affinity-purified antibody as a probe of RNA polymerase II subunit structure. 
  • Allele-specific distribution of RNA polymerase II on female X chromosomes. 
  • Alpha-amanitin-resistant D. melanogaster with an altered RNA polymerase II. 
  • Alternative somatic and germline gene-regulatory strategies during starvation-induced developmental arrest. 
  • Amanitin-resistant RNA polymerase II mutations are in the enzyme's largest subunit. 
  • An activity necessary for in vitro transcription is a DNase inhibitor. 
  • An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. 
  • Analyses of promoter-proximal pausing by RNA polymerase II on the hsp70 heat shock gene promoter in a Drosophila nuclear extract. 
  • Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. 
  • Assaying CTD kinases in vitro and phosphorylation-modulated properties of RNA polymerase II in vivo. 
  • Ataxia telangiectasia mutant protein activates c-Abl tyrosine kinase in response to ionizing radiation. 
  • BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation. 
  • C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats. 
  • CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. 
  • CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. 
  • Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. 
  • Co-transcriptional splicing of pre-messenger RNAs: considerations for the mechanism of alternative splicing. 
  • Coactivator AIB1 links estrogen receptor transcriptional activity and stability. 
  • Coordination of replication and transcription along a Drosophila chromosome. 
  • Cotranscriptional association of mRNA export factor Yra1 with C-terminal domain of RNA polymerase II. 
  • Cyclophilin A and Ess1 interact with and regulate silencing by the Sin3-Rpd3 histone deacetylase. 
  • Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription. 
  • Direct visualization of cardiac transcription factories reveals regulatory principles of nuclear architecture during pathological remodeling. 
  • Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin. 
  • Distribution of RNA polymerase on Drosophila polytene chromosomes as studied by indirect immunofluorescence. 
  • Drosophila RNA polymerase II mutants that affect transcription elongation. 
  • Dye-ligand affinity chromatography of RNA polymerase II. 
  • Dynamic interaction between a Drosophila transcription factor and RNA polymerase II. 
  • Dynamics of BAF-Polycomb complex opposition on heterochromatin in normal and oncogenic states. 
  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. 
  • Elongation by Drosophila RNA polymerase II. Transcription of 3'-extended DNA templates. 
  • Eukaryotic gene transcription with purified components. 
  • Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. 
  • Evaluating group I intron catalytic efficiency in mammalian cells. 
  • Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. 
  • FSH-induction of androgen binding protein in testes of Sertoli cell-only rats. 
  • Fractionation of transcription factors for RNA polymerase II from Drosophila Kc cell nuclear extracts. 
  • Functional organization of polytene chromosomes. 
  • Functional studies of the carboxy-terminal repeat domain of Drosophila RNA polymerase II in vivo. 
  • Genetic and biochemical characterization of mutants at an RNA polymerase II locus in D. melanogaster. 
  • Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain. 
  • Getting a grip on the CTD of Pol II. 
  • Heat shock-induced appearance of RNA polymerase II in karyoskeletal protein-enriched (nuclear "matrix") fractions correlates with transcriptional shutdown in Drosophila melanogaster. 
  • Heat-shock-specific phosphorylation and transcriptional activity of RNA polymerase II. 
  • Human promoters are intrinsically directional. 
  • Identification of a structural gene for a RNA polymerase II polypeptide in Drosophila melanogaster and mammalian species. 
  • Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. 
  • Identification of gemin5 as a novel 7-methylguanosine cap-binding protein. 
  • Identification, molecular cloning, and mutagenesis of Saccharomyces cerevisiae RNA polymerase genes. 
  • Identifying a transcription factor interaction site on RNA polymerase II. 
  • Identifying phosphoCTD-associating proteins. 
  • Immunological studies of RNA polymerase II using antibodies to subunits of Drosophila and wheat germ enzyme. 
  • Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota). 
  • In vitro proteolysis of a large subunit of Drosophila melanogaster RNA polymerase B. 
  • JMJD5 couples with CDK9 to release the paused RNA polymerase II. 
  • JMJD6 cleaves MePCE to release positive transcription elongation factor b (P-TEFb) in higher eukaryotes. 
  • Juglone, an inhibitor of the peptidyl-prolyl isomerase Pin1, also directly blocks transcription. 
  • Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. 
  • Localization of RNA polymerase in polytene chromosomes of Drosophila melanogaster. 
  • Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. 
  • Long Noncoding RNA Ceruloplasmin Promotes Cancer Growth by Altering Glycolysis. 
  • Mapping mutations in genes encoding the two large subunits of Drosophila RNA polymerase II defines domains essential for basic transcription functions and for proper expression of developmental genes. 
  • Modulation of RNA polymerase II elongation efficiency by C-terminal heptapeptide repeat domain kinase I. 
  • Molecular cloning of sequences from a Drosophila RNA polymerase II locus by P element transposon tagging. 
  • Molecular determinants for enzalutamide-induced transcription in prostate cancer. 
  • Mutation of MeCP2 alters transcriptional regulation of select immediate-early genes. 
  • New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. 
  • New species and distribution records for Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, with a key to the lowland neotropical taxa. 
  • New species of Clavulina (Cantharellales, Basidiomycota) with resupinate and effused basidiomata from the Guiana Shield. 
  • Noncoding Transcription Is a Driving Force for Nucleosome Instability in spt16 Mutant Cells. 
  • Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding. 
  • PGC-1α senses the CBC of pre-mRNA to dictate the fate of promoter-proximally paused RNAPII. 
  • Perspectives on Unidirectional versus Divergent Transcription. 
  • Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. 
  • Phase I and pharmacokinetic study of 3'-C-ethynylcytidine (TAS-106), an inhibitor of RNA polymerase I, II and III,in patients with advanced solid malignancies. 
  • Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3'-End formation. 
  • Phosphorylated MED1 links transcription recycling and cancer growth. 
  • Phosphorylation and functions of the RNA polymerase II CTD. 
  • Phosphorylation dependence of the initiation of productive transcription of Balbiani ring 2 genes in living cells. 
  • Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. 
  • Phosphorylation of RNA polymerase II CTD fragments results in tight binding to the WW domain from the yeast prolyl isomerase Ess1. 
  • Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota). 
  • Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. 
  • Plant promoter-proximal pausing? 
  • Pol II docking and pausing at growth and stress genes in C. elegans. 
  • Positive patches and negative noodles: linking RNA processing to transcription? 
  • Properties of a Drosophila RNA polymerase II elongation factor. 
  • Properties of mutationally altered RNA polymerases II of Drosophila. 
  • Protein secondary structure determination by constrained single-particle cryo-electron tomography. 
  • Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II. 
  • Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. 
  • Protonation of the neutral repeats of the RNA polymerase II CTD. 
  • Purification of the three nuclear RNA polymerases from Neurospora crassa. 
  • RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription. 
  • RNA Pol II accumulates at promoters of growth genes during developmental arrest. 
  • RNA polymerase B (or II) in heat induced puffs of Drosophila polytene chromosomes. 
  • Regulation of Co-transcriptional Pre-mRNA Splicing by m⁶ A through the Low-Complexity Protein hnRNPG. 
  • Reverse genetics of Drosophila RNA polymerase II: identification and characterization of RpII140, the genomic locus for the second-largest subunit. 
  • Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae. 
  • Sequence specificity incompletely defines the genome-wide occupancy of Myc. 
  • Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats. 
  • Site-specific silencing of regulatory elements as a mechanism of X inactivation. 
  • Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts. 
  • Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1. 
  • Specific interaction of the transcription elongation regulator TCERG1 with RNA polymerase II requires simultaneous phosphorylation at Ser2, Ser5, and Ser7 within the carboxyl-terminal domain repeat. 
  • Stimulation of mitotic recombination events by high levels of RNA polymerase II transcription in yeast. 
  • Structural basis of core promoter recognition in a primitive eukaryote. 
  • Structural studies on Neurospora RNA polymerases and associated proteins. 
  • Structure of the eukaryotic transcription apparatus: features of the gene for the largest subunit of Drosophila RNA polymerase II. 
  • The C-terminal repeat domain of RNA polymerase II largest subunit is essential in vivo but is not required for accurate transcription initiation in vitro. 
  • The Ess1 prolyl isomerase is linked to chromatin remodeling complexes and the general transcription machinery. 
  • The MTE, a new core promoter element for transcription by RNA polymerase II. 
  • The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3' cleavage/polyadenylation through the processing component Pti1p. 
  • The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. 
  • The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. 
  • The carboxyl-terminal repeat domain of RNA polymerase II is not required for transcription factor Sp1 to function in vitro. 
  • The essential sequence elements required for RNAP II carboxyl-terminal domain function in yeast and their evolutionary conservation. 
  • The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. 
  • Thyroid hormone-regulated target genes have distinct patterns of coactivator recruitment and histone acetylation. 
  • To grow or not to grow: nutritional control of development during Caenorhabditis elegans L1 arrest. 
  • Transcription errors induce proteotoxic stress and shorten cellular lifespan. 
  • Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling. 
  • Yeast screens identify the RNA polymerase II CTD and SPT5 as relevant targets of BRCA1 interaction. 
  • cis-Proline-mediated Ser(P)5 dephosphorylation by the RNA polymerase II C-terminal domain phosphatase Ssu72. 
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  Keywords of People

  • Baugh, L. Ryan, Associate Professor of Biology, Biology
  • Guan, Ziqiang, Research Professor in Biochemistry, Biochemistry
  • Reddy, Timothy E, Associate Professor of Biostatistics & Bioinformatics,, Molecular Genetics and Microbiology