TY - JOUR. T1 - Phosphorylation of the carboxy-terminal repeat domain in RNA polymerase II by cyclin-dependent kinases is sufficient to inhibit transcription. AU - Gebara, Maha M.. AU - Sayre, Michael H.. AU - Corden, Jeffry L.. PY - 1997/3/1. Y1 - 1997/3/1. N2 - Cdc2 kinase triggers the entry of mammalian cells into mitosis, the only cell phase in which transcription is globally repressed. We show here that Cdc2 kinase phosphorylates components of the RNA polymerase II transcription machinery including the RNA polymerase II carboxy-terminal repeat domain (CTD). To test specifically the effect of CTD phosphorylation by Cdc2 kinase, we used a yeast in vitro transcription extract that is dependent on exogenous RNA polymerase II that contains a CTD. Phosphorylation was carried out using immobilized Cdc2 so that the kinase could be removed from the phosphorylated polymerase. ATPγS and Cdc2 kinase were used to produce an RNA polymerase 110 that was not detectably dephosphorylated in the ...
Yeast RNA polymerase II initiation factor b copurifies with three polypeptides of 85, 73, and 50 kilodaltons and with a protein kinase that phosphorylates the carboxyl-terminal repeat domain (CTD) of the largest polymerase subunit. The gene that encodes the 73-kilodalton polypeptide, designated TFB1, was cloned and found to be essential for cell growth. The deduced protein sequence exhibits no similarity to those of protein kinases. However, the sequence is similar to that of the 62-kilodalton subunit of the HeLa transcription factor BFT2, suggesting that this factor is the human counterpart of yeast factor b. Immunoprecipitation experiments using antibodies to the TFB1 gene product demonstrate that the transcriptional and CTD kinase activities of factor b are closely associated with an oligomer of the three polypeptides. Photoaffinity labeling with 3-O-(4-benzoyl)benzoyl-ATP (adenosine triphosphate) identified an ATP-binding site in the 85-kilodalton polypeptide, suggesting that the ...
SCU22109 U22109 1948bp DNA PLN 26-APR-1995 Saccharomyces cerevisiae Ytp1p (YTP1) gene, complete cds. YTP1; Ytp1p. SCU22156 U22156 3680bp DNA PLN 26-APR-1995 Saccharomyces cerevisiae Hfm1p (HFM1) gene, complete cds. HFM1; Hfm1p. SCU22361 U22361 5599bp DNA PLN 26-APR-1995 Saccharomyces cerevisiae Rlr1p (RLR1) gene, complete cds. RLR1; Rlr1p. SCU23811 U23811 1494bp DNA PLN 26-APR-1995 Saccharomyces cerevisiae RNA polymerase II holoenzyme component (SRB7) gene, complete cds. SRB7; RNA polymerase II holoenzyme component. SCU23812 U23812 4849bp DNA PLN 26-APR-1995 Saccharomyces cerevisiae RNA polymerase II holoenzyme component (SRB9) gene, complete cds. SRB9; RNA polymerase II holoenzyme component. SCU24129 U24129 2965bp DNA PLN 26-APR-1995 Saccharomyces cerevisiae sporulation-specific septin (SPR3) gene, complete cds. SPR3; sporulation-specific septin. SCU24143 U24143 298bp mRNA PLN 26-APR-1995 Saccharomyces cerevisiae ribosomal protein S12 mRNA, partial cds. S12; ribosomal protein S12. SCU24144 ...
The unique C-terminal repeat domain (CTD) of the largest subunit (IIa) of eukaryotic RNA polymerase II consists of multiple repeats of the heptapeptide consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. The number of repeats ranges from 26 in yeast to 42 in Drosophila to 52 in mouse. The CTD is essential in vivo, but its structure and function are not yet understood. The CTD can be phosphorylated at multiple serine and threonine residues, generating a form of the largest subunit (II0) with markedly reduced mobility in NaDodSO4/polyacrylamide gels. To investigate this extensive phosphorylation, which presumably modulates functional properties of RNA polymerase II, we began efforts to purify a specific CTD kinase. Using CTD-containing fusion proteins as substrates, we have purified a CTD kinase from the yeast Saccharomyces cerevisiae. The enzyme extensively phosphorylates the CTD portion of both the fusion proteins and intact subunit IIa, producing products with reduced electrophoretic mobilities. ...
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May play a role as a target recruitment subunit in E3 ubiquitin-protein ligase complexes and thus in ubiquitination and subsequent proteasomal degradation of target proteins.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways.
Antibodies for proteins involved in RNA polymerase II transcription factor binding pathways, according to their Panther/Gene Ontology Classification
The tandem SH2 domains of Spt6 use novel mechanisms to bind unexpected phosphorylated serine and threonine residues in the RNA polymerase II linker to recruit Spt6 to sites of transcription and maintain repressive chromatin.
ChIP-chip was performed to identify the genomic binding locations for the termination factors Nrd1, and Rtt103, and for RNA polymerase (Pol) II phosphorylated at the tyrosine 1 and threonine 4 position of its C-terminal domain (CTD). In different phases of the transcription cycle, Pol II recruits different factors via its CTD, which consists of heptapeptide repeats with the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Here we show that the CTD of transcribing yeast Pol II is phosphorylated at Tyr1, and that this impairs recruitment of termination factors. Tyr1 phosphorylation levels rise downstream of the transcription start site (TSS), and decrease before the polyadenylation (pA) site. Tyr1-phosphorylated gene bodies are depleted of CTD-binding termination factors Nrd1, Pcf11, and Rtt103. Tyr1 phosphorylation blocks CTD binding by these termination factors, but stimulates binding of elongation factor Spt6. These results show that CTD modifications can not only stimulate but also block factor
RNA polymerase II large subunit; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. NRPB1 is part of the core element with the central large cleft, the cl [...] (1839 aa ...
387448814 - EP 0851912 A4 2000-01-05 - NOVEL FACTORS WHICH MODIFY GENE TRANSCRIPTION AND METHODS OF USE THEREFOR - [origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.[origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.
Antibodies for proteins involved in RNA polymerase II core promoter sequence-specific DNA binding pathways, according to their Panther/Gene Ontology Classification
GO Terms Descrition:, periodic partitioning by pair rule gene, central nervous system development, RNA polymerase II distal enhancer sequence-specific DNA binding, positive regulation of transcription from RNA polymerase II promoter, trunk segmentation, cell fate specification, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription, regulation of transcription from RNA polymerase II promoter, blastoderm segmentation, negative regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-templated, sequence-specific DNA binding transcription factor activity, nucleus, sequence-specific DNA binding, gonadal mesoderm development, segmentation, posterior head segmentation, germ cell migration ...
The DNA in eukaryotes is arranged in fibres of chromatin. The chromatin may be more or less compacted and the degree of condensation of the chromatin affects the accessibility of the DNA. The accessibility of the DNA, in turn, affects transcription and gene regulation. Genes within inaccessible DNA are commonly repressed whereasgenes within accessible DNA are active and expressed. This thesis concerns the interplay between chromatin and transcription with focus on the function of the RNA polymerase II (pol II) subunit Rpb7. We have demonstrated that processing of centromeric transcripts by the ribonuclease III family protein Dcr1 is required for heterochromatin formation at the centromeres of Schizosaccharomyces pombe. A point mutation in the pol II subunit Rpb7 caused a specific defect in centromeric heterochromatin formation. We have shown i) that the centromeric transcripts that accumulate in dcr1delta cells are products of pol II, ii) the rpbG150D mutation is deficient in recognition and/or ...
DNA-directed RNA polymerase II subunit RPB7; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. NRPB7 is part of a subcomplex with NRPB4 that binds to a pocket formed by NRPB1, NRPB2 and NRPB6 at the base of the clamp element. The NRBP4-NRPB7 subcomplex [...] (176 aa ...
Human RNA polymerase II is shown to be associated with a 3--|5 exonuclease activity that removes nucleoside 5-monophosphates from the 3 end of the transcripts in isolated ternary complexes. This activity is stimulated by SII, a protein that acts as a transcription elongation factor in vitro. In addition, we show that another transcription factor, TFIIF, stimulates a competing pyrophosphorolysis reaction. These findings raise interesting questions about the roles of these activities in vivo, including the possibility that this RNA polymerase may proofread the nascent transcript.
Rabbit recombinant monoclonal RNA polymerase II CTD repeat YSPTSPS (phospho S1801) antibody [EP1510Y] validated for WB, IP, IHC, ICC/IF and tested in Human…
Buy our Recombinant Human RNA Polymerase II p14.5 protein. Ab81852 is a full length protein produced in Escherichia coli and has been validated in SDS-PAGE…
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as transcription factories, but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes.
GO Terms Descrition:, biological_process, molecular_function, DNA binding, cellular component assembly, macromolecular complex assembly, ion binding, chromosome segregation, biosynthetic process, cellular nitrogen compound metabolic process, cellular_component, nucleolus, organelle, nucleoplasm, nucleus, protein binding transcription factor activity, nucleic acid binding transcription factor activity, chromosome, negative regulation of transcription from RNA polymerase II promoter, chromosome, centromeric region, condensed chromosome, RNA polymerase II core promoter proximal region sequence-specific DNA binding, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription, sequence-specific DNA binding transcription factor activity, transcription corepressor activity, protein binding, transcription, DNA-templated, zinc ion binding, positive regulation of gene expression, chromatin modification, ...
The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters. TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10-20% of human promoters have TATA boxes. Therefore, TBP is probably not the only protein involved in positioning RNA polymerase II. TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β ...
Author Summary The transcription of eukaryotic genes involves a highly ordered series of events, including the recruitment of RNA polymerase to promoters, the production of the RNA transcript, and termination. These events are coordinated with changes in chromatin structure that allow regulatory proteins and RNA polymerase to access the DNA template. The recruitment of RNA polymerase II to promoters is rate-limiting for the expression of most eukaryotic genes. However, RNA polymerase often pauses or stalls a short distance downstream of promoters, providing an additional step at which transcription can be regulated. In this study, we present evidence suggesting that a chromatin-remodeling factor, KIS-L, activates transcription by counteracting promoter-proximal pausing in Drosophila. KIS-L also counteracts histone H3 lysine 27 methylation-a covalent modification of chromatin involved in hereditable gene silencing. Our findings provide a plausible explanation for the developmental abnormalities
MCM Proteins Are Associated with RNA Polymerase II Holoenzyme: MCMs are a family of proteins related to ATP-dependent helicases that bind to origin recognition
We have recently cloned a new member of the human Ser/Arg-rich superfamily (SR) of pre-mRNA splicing factors, SR-A1. Members of the SR family of proteins have been shown to interact with the C-terminal domain (CTD) of the large subunit of RNA polymerase II, and participate in pre-mRNA splicing. The largest subunit of RNA polymerase II contains at the carboxy-terminus a peculiar repetitive sequence that consists of 52 tandem repeats of the consensus motif Tyr-Ser-Pro-Thr-Ser-Pro-Ser, referred to as the CTD. There is evidence that SR protein splicing factors are involved in cancer pathobiology through their involvement in alternative processing events. The CTD of human SR-A1 protein (aa 1187-1312), containing a conserved CTD-interaction domain and bearing a decahistidine (His10) tag was produced by DNA recombinant overexpression techniques in Escherichia coli from the vector pET16b and it was localized in the periplasmic space. The protein was further purified using a HiTrap chelating column and its
How does RNA polymerase II coordinate the synthesis of messenger RNA, resulting in proper cellular regulation and organismic development? The sessions will cover new findings in transcriptional initiation, elongation and termination and the role of RNA polymerase II, its C-terminal domain and the associated factors in this process. New findings on the roles of chromatin, their interacting proteins and post-translational modifications, their numerous transcriptional properties and their role in development also will be addressed. The plenary lecture will be presented by Ramin Shiekhattar, who will describe his work on the functions of long noncoding RNAs in transcriptional regulation, development and disease pathogenesis. This years meeting represents the 10th anniversary of this important and influential conference. ...
DNA-directed RNA polymerase II subunit RPB1, also known as RPB1, is an enzyme that in humans is encoded by the POLR2A gene. This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene contains a carboxy terminal domain composed of heptapeptide repeats that are essential for polymerase activity. These repeats contain serine and threonine residues that are phosphorylated in actively transcribing RNA polymerase. In addition, this subunit, in combination with several other polymerase subunits, forms the DNA-binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA. POLR2A has been shown to interact with: BRCA1, CREBBP, CTDP1, CDK8, GTF2B, GTF2F1, GTF2H4, MED21, MED26, PCAF, POLR2C, POLR2E, POLR2H, POLR2L, PQBP1, SMARCA2, SMARCA4 SMARCB1, SMYD3, SND1, SUPT5H, TAF11, TBP, TCEA1, TCERG1, and ZNF74. GRCm38: Ensembl release 89: ENSMUSG00000005198 - Ensembl, May 2017 "Human ...
Regulatory component of the SET1 complex implicated in the tethering of this complex to transcriptional start sites of active genes. Facilitates histone H3 Lys-4 methylation via recruitment of the SETD1A or SETD1B to the Ser-5 phosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A). Component of PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase ...
Cdc14 is an essential phosphatase in yeast but its role in the mammalian cell cycle remains obscure. We report here that Cdc14b-knockout cells display unscheduled induction of multiple cell cycle regulators resulting in early entry into DNA replication and mitosis from quiescence. Cdc14b dephosphorylates Ser5 at the C-terminal domain (CTD) of RNA polymerase II, a major substrate of cyclin-dependent kinases. Lack of Cdc14b results in increased CTD-Ser5 phosphorylation, epigenetic modifications that mark active chromatin, and transcriptional induction of cell cycle regulators. These data suggest a function for mammalian Cdc14 phosphatases in the control of transcription during the cell cycle ...
positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process - Ontology Report - Rat Genome Database
INTS4 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690) (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008 ...
Spt4-Spt5 and TFIIS functions depend on the CTD and CTD modifying enzymes: The data presented here demonstrate that the functions of Spt4-Spt5 and TFIIS are interrelated with those of the Pol II CTD and the enzymes that modify its phosphorylation state. Cells that are defective for Spt4-Spt5 or TFIIS function show an increased dependence upon the length and composition of the CTD, Kin28, Bur1, Ctk1, and Fcp1. In contrast to these genetic interactions, the srb10Δ mutation caused new phenotypes only when combined with spt5-242. Thus, the interdependence of TFIIS and Spt4-Spt5 on the Srb10 CTD kinase, which is implicated in negative regulation of preinitiation complex assembly (Hengartneret al. 1998; Sunet al. 1998), is less clear.. How does the CTD affect Spt4-Spt5 and TFIIS function? Several models have been proposed to explain the dependence of DSIF on P-TEFb. In one, phosphorylation of the CTD by P-TEFb is proposed to prevent DSIF from binding Pol II and inhibiting elongation (Wadaet al. ...
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.
Pol II (RNA polymerase II) transcribes the genes encoding proteins and non-coding snRNAs (small nuclear RNAs). The largest subunit of Pol II contains a distinctive CTD (C-terminal domain) comprising a repetitive heptad amino acid sequence, Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. This domain is now known to play a major role in the processes of transcription and co-transcriptional RNA processing in expression of both snRNA and protein-coding genes. The heptapeptide repeat unit can be extensively modified in vivo and covalent modifications of the CTD during the transcription cycle result in the ordered recruitment of RNA-processing factors. The most studied modifications are the phosphorylation of the serine residues in position 2 and 5 (Ser2 and Ser5), which play an important role in the co-transcriptional processing of both mRNA and snRNA. An additional, recently identified CTD modification, phosphorylation of the serine residue in position 7 (Ser7) of the heptapeptide, is however specifically ...
beta-Catenin signaling plays an important role in the development of many organisms and has a key part in driving the malignant transformation of epithelial cells comprising a variety of cancers. beta-Catenin can activate gene expression through its association with transcription factors of the lymp …
RNA polymerase II elongation complex. Computer model showing yeast RNA polymerase (grey) complexed with DNA (green) and RNA (pink). This enzyme synthesises a complementary mRNA (messenger ribonucleic acid) strand from a strand of DNA (deoxyribonucleic acid) during a DNA transcription. The RNA polymerase molecule uses the original DNA strand as a template for the mRNA. - Stock Image C035/5381
Cells are subjected to dramatic changes of gene expression upon environmental changes. Stresscauses a general down-regulation of gene expression together with the induction of a set of stress-responsivegenes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription uponosmostress in yeast. Genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1 showed that stress induced major changes in RNA Pol II localization, with a shift toward stress-responsive genes relative to housekeeping genes. RNA Pol II relocalization required Hog1, which was also localized to stress-responsive loci. In addition to RNA Pol II-bound genes, Hog1 also localized to RNA polymerase III-bound genes, pointing to a wider role for Hog1 in transcriptional control than initially expected. Interestingly, an increasing association of Hog1 with stressresponsive genes was strongly correlated with chromatin remodeling and increased gene expression. Remarkably, MNase-Seq ...
What is the difference between Prokaryotic and Eukaryotic RNA Polymerase? Prokaryotic RNA polymerase produces polycistronic mRNA. Eukaryotic RNA polymerase...
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As ovarian tumors progress, they undergo a process of dedifferentiation, allowing adaptive changes in growth and morphology that promote metastasis and chemoresistance. Herein, we outline a hypothesis that TATA-box binding protein (TBP) associated factors (TAFs), which compose the RNA Polymerase II initiation factor, TFIID, contribute to regulation of dedifferentiation states in ovarian cancer. Numerous studies demonstrate that TAFs regulate differentiation and proliferation states; their expression is typically high in pluripotent cells and reduced upon differentiation. Strikingly, TAF2 exhibits copy number increases or mRNA overexpression in 73% of high grade serous ovarian cancers (HGSC). At the biochemical level, TAF2 directs TFIID to TATA-less promoters by contact with an Initiator element, which may lead to the deregulation of the transcriptional output of these tumor cells. TAF4, which is altered in 66% of HGSC, is crucial for the stability of the TFIID complex and helps drive
Specific assembly of ribonucleoprotein complexes is essential in controlling various cellular functions including gene regulation. Diverse scaffolds containing proteins or nucleic acids could play key roles in stabilizing specific ribonucleoprotein complexes by enhancing protein-protein or RNA-protein interactions. One such example is the assembly of active RNA polymerase II transcription elongation complex originating from HIV-1 long terminal repeat promoter that involves HIV-1-encoded Tat protein and viral mRNA structure, trans-activation responsive RNA, and human CyclinT1 which is a subunit of the positive transcription elongation factor complex b. By using genetically encoded fluorescent proteins fused with Tat and human CyclinT1, here we demonstrate that human CyclinT1 was diffused throughout the nucleus and specific interactions between Tat and human CyclinT1 altered the localization of human CyclinT1 to specific nuclear foci. We also found that trans-activation responsive RNA enhanced protein
Liu, X.; Farnung, L.; Wigge, C.; Cramer, P.: Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by α-amanitin. Journal of Biological Chemistry 293 (19), pp. 7189 - 7194 (2018 ...
ELP3: Elp3, a yeast A-type HAT, appears to have a direct role in transcription in that it is part of the RNA polymerase II holoenzyme and is involved in transcriptional elongation. In S. cerevisiae, the three-subunit elongator complex binds tightly to RNA polymerase II and its hyperphosphorylated C-terminal repeat domain (CTD), participating in an elongation-competent form of holoenzyme. Elp3, the smallest elongator subunit, was identified by peptide mass spectrometry and found to have GNAT homology. Because of its GNAT homology, recombinant Elp3 was produced from insect cells and tested for HAT activity in in-gel assays. Under these conditions, Elp3 was able to acetylate all four core histones when presented with them individually (1) Reference ...
Identification and characterization of Mediator-containing RNA polymerase II holoenzyme. As an undergraduate student with Henry Pitot at the University of Wisconsin, I helped characterize the gene encoding the barbiturate-induced aldehyde dehydrogenase from rat liver. This project exposed me to the compelling idea that an environmental cue, in this case phenobarbital, can dramatically change the gene-expression profile of the hepatocyte. My Ph.D. thesis research with Rick Young at the Whitehead Institute/MIT pursued my growing fascination with the complicated process of how genes get turned on. I identified an "initiation factor" required for RNA polymerase II to begin transcription of protein-coding genes in yeast. I demonstrated that this factor was part of a large complex, which we called the SRB complex (for suppressor of RNA polymerase B/II), contemporaneously discovered and named Mediator by Roger Kornbergs lab. I went on to purify RNA polymerase II in complex with SRB complex/Mediator ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): MicroRNAs (miRNAs) constitute a large family of noncod-ing RNAs that function as guide molecules in diverse gene silencing pathways. Current efforts are focused on the regulatory function of miRNAs, while little is known about how these unusual genes themselves are regulated. Here we present the first direct evidence that miRNA genes are transcribed by RNA polymerase II (pol II). The primary miRNA transcripts (pri-miRNAs) contain cap structures as well as poly(A) tails, which are the unique properties of class II gene transcripts. The treatment of human cells with a-amanitin decreased the level of pri-miRNAs at a concentration that selectively inhibits pol II activity. Furthermore, chromatin immunoprecipitation analyses show that pol II is physically associated with a miRNA promoter. We also describe, for the first time, the detailed structure of a miRNA gene by determining the promoter and the terminator of mir-23aB27aB24-2.
Transition from the closed to the open promoter complex happens by separation of the DNA strands to form an unwound DNA region. Once the transcription bubble forms the template single strand DNA gets positioned in the active center of Pol II. RNA synthesis then can initiate from the transcription start site. The initially transcribing complex (ITC) is unstable and releases short RNAs during abortive initiation (not shown in the movie). When the RNA reaches a certain length, initiation factors are released, and a stable elongation complex (EC) is formed. Elongation complex contains a DNA-RNA hybrid of eight to nine base pairs. During transcription elongation, the EC repeatedly performs the nucleotide addition cycle (NAC) to attach a nucleotide to the growing messenger RNA (mRNA) chain by catalyzing DNA template-directed formation of an RNA phosphodiester bond. Errors do occur during RNA transcription and must be corrected to prevent synthesis of mutated, nonfunctional proteins that possibly ...
Che-1 is a RNA polymerase II binding protein involved in the regulation of gene transcription, and in response to DNA damage promotes p53 transcription. In this study, we investigated whether Che-1 regulates mutant p53 expression. We found that Che-1 is required for sustaining mutant p53 expression in several cancer cell lines, and Che-1 depletion by siRNA induces apoptosis both in vitro and in vivo. Notably, loss of Che-1 activates DNA damage checkpoint response and induces transactivation of p73. Therefore, these findings suggest a new therapeutic approach that allowing simultaneous modulation of p73 and mutant p53 levels might be used to target the large fraction of human tumors harboring p53 mutations.. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2983. ...
In this post I have a look at the ENCODE RNA polymerase II ChIP-seq data and overlay the ChIP-seq peaks onto RefSeq transcription start sites.
At Novus Biologicals, we recently added a new RNA Polymerase II antibody (clone 4H8) to our antibody catalog. RNAPII is an essential transcription enzyme,
A comparison was drawn between the action of Cibacron Blue F3GA on the enzymic activity of DNA-dependent RNA polymerases from different sources, e.g. Escherichia coli, calf thymus and wheat germ (polymerase II). Sensitivity towards this inhibitor was determined for polymer formation and primed abortive synthesis of trinucleotide UpApU. In case of E. coli polymerase and wheat germ polymerase II the dye inhibits both polymer formation and abortive synthesis. Calf thymus polymerase II is inhibited only in the polymerisation step. The primed initiation reaction was found to be resistant towards the dye. In case of E. coli polymerase and wheat germ polymerase II the sensitive step is the formation of internucleotide bond whereas in case of calf thymus polymerase II the translocation of the enzyme is influenced. An analysis of kinetic data indicates more than one binding site for the dye on RNA polymerase II from calf thymus and wheat germ. Cibacron blue does not inhibit specific transcription ...