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Journal articles on the topic 'Transcription factors RNA polymerases'

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Published: 4 June 2021

Last updated: 4 February 2022

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1

Tuteja, Renu, Abulaish Ansari, and Virander Singh Chauhan. "Emerging Functions of Transcription Factors in Malaria Parasite." Journal of Biomedicine and Biotechnology 2011 (2011): 1–6. http://dx.doi.org/10.1155/2011/461979.

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Transcription is a process by which the genetic information stored in DNA is converted into mRNA by enzymes known as RNA polymerase. Bacteria use only one RNA polymerase to transcribe all of its genes while eukaryotes contain three RNA polymerases to transcribe the variety of eukaryotic genes. RNA polymerase also requires other factors/proteins to produce the transcript. These factors generally termed as transcription factors (TFs) are either associated directly with RNA polymerase or add in building the actual transcription apparatus. TFs are the most common tools that our cells use to contro

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2

Thomm, Michael, Christoph Reich, Sebastian Grünberg, and Souad Naji. "Mutational studies of archaeal RNA polymerase and analysis of hybrid RNA polymerases." Biochemical Society Transactions 37, no. 1 (2009): 18–22. http://dx.doi.org/10.1042/bst0370018.

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The recent success in reconstitution of RNAPs (RNA polymerases) from hyperthermophilic archaea from bacterially expressed purified subunits opens the way for detailed structure–function analyses of multisubunit RNAPs. The archaeal enzyme shows close structural similarity to eukaryotic RNAP, particularly to polymerase II, and can therefore be used as model for analyses of the eukaryotic transcriptional machinery. The cleft loops in the active centre of RNAP were deleted and modified to unravel their function in interaction with nucleic acids during transcription. The rudder, lid and fork 2 clef

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3

Tan, Adelene Y., and James L. Manley. "TLS Inhibits RNA Polymerase III Transcription." Molecular and Cellular Biology 30, no. 1 (2009): 186–96. http://dx.doi.org/10.1128/mcb.00884-09.

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ABSTRACT RNA transcription by all the three RNA polymerases (RNAPs) is tightly controlled, and loss of regulation can lead to, for example, cellular transformation and cancer. While most transcription factors act specifically with one polymerase, a small number have been shown to affect more than one polymerase to coordinate overall levels of transcription in cells. Here we show that TLS (translocated in liposarcoma), a protein originally identified as the product of a chromosomal translocation and which associates with both RNAP II and the spliceosome, also represses transcription by RNAP III

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4

Szafranski, Przemyslaw, and W. Jerzy Smagowicz. "Relative Affinities of Nucleotide Substrates for the Yeast tRNA Gene Transcription Complex." Zeitschrift für Naturforschung C 47, no. 3-4 (1992): 320–22. http://dx.doi.org/10.1515/znc-1992-3-426.

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Abstract Apparent Michaelis constants for nucleotides in transcription of yeast tRN Agene by hom ologous RNA polymerase III with auxiliary protein factors, were found to be remarkably higher in initiation than in elongation of RNA chain. This supports presumptions regarding topological similarities between catalytic centers of bacterial and eukaryotic RNA polymerases.

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5

Gridasova, Anastasia A., and R. William Henry. "The p53 Tumor Suppressor Protein Represses Human snRNA Gene Transcription by RNA Polymerases II and III Independently of Sequence-Specific DNA Binding." Molecular and Cellular Biology 25, no. 8 (2005): 3247–60. http://dx.doi.org/10.1128/mcb.25.8.3247-3260.2005.

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ABSTRACT Human U1 and U6 snRNA genes are transcribed by RNA polymerases II and III, respectively. While the p53 tumor suppressor protein is a general repressor of RNA polymerase III transcription, whether p53 regulates snRNA gene transcription by RNA polymerase II is uncertain. The data presented herein indicate that p53 is an effective repressor of snRNA gene transcription by both polymerases. Both U1 and U6 transcription in vitro is repressed by recombinant p53, and endogenous p53 occupancy at these promoters is stimulated by UV light. In response to UV light, U1 and U6 transcription is stro

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6

Leśniewska, Ewa, and Magdalena Boguta. "Novel layers of RNA polymerase III control affecting tRNA gene transcription in eukaryotes." Open Biology 7, no. 2 (2017): 170001. http://dx.doi.org/10.1098/rsob.170001.

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RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases. Novel concepts concerning Pol III functioning involve recruitment of ge

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7

Gomez-Roman, Natividad, Zoë A. Felton-Edkins, Niall S. Kenneth, et al. "Activation by c-Myc of transcription by RNA polymerases I, II and III." Biochemical Society Symposia 73 (January 1, 2006): 141–54. http://dx.doi.org/10.1042/bss0730141.

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The proto-oncogene product c-Myc can induce cell growth and proliferation. It regulates a large number of RNA polymerase II-transcribed genes, many of which encode ribosomal proteins, translation factors and other components of the biosynthetic apparatus. We have found that c-Myc can also activate transcription by RNA polymerases I and III, thereby stimulating production of rRNA and tRNA. As such, c-Myc may possess the unprecedented capacity to induce expression of all ribosomal components. This may explain its potent ability to drive cell growth, which depends on the accumulation of ribosomes

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8

Huang, Sui, Thomas J. Deerinck, Mark H. Ellisman, and David L. Spector. "The Perinucleolar Compartment and Transcription." Journal of Cell Biology 143, no. 1 (1998): 35–47. http://dx.doi.org/10.1083/jcb.143.1.35.

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The perinucleolar compartment (PNC) is a unique nuclear structure localized at the periphery of the nucleolus. Several small RNAs transcribed by RNA polymerase III and two hnRNP proteins have been localized in the PNC (Ghetti, A., S. Piñol-Roma, W.M. Michael, C. Morandi, and G. Dreyfuss. 1992. Nucleic Acids Res. 20:3671–3678; Matera, A.G., M.R. Frey, K. Margelot, and S.L. Wolin. 1995. J. Cell Biol. 129:1181– 1193; Timchenko, L.T., J.W. Miller, N.A. Timchenko, D.R. DeVore, K.V. Datar, L. Lin, R. Roberts, C.T. Caskey, and M.S. Swanson. 1996. Nucleic Acids Res. 24: 4407–4414; Huang, S., T. Deerin

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9

Vanhamme, Luc. "Trypanosome RNA Polymerases and Transcription Factors: Sensible Trypanocidal Drug Targets?" Current Drug Targets 9, no. 11 (2008): 979–96. http://dx.doi.org/10.2174/138945008786786064.

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10

Magill, Christine P., Stephen P. Jackson, and Stephen D. Bell. "Identification of a Conserved Archaeal RNA Polymerase Subunit Contacted by the Basal Transcription Factor TFB." Journal of Biological Chemistry 276, no. 50 (2001): 46693–96. http://dx.doi.org/10.1074/jbc.c100567200.

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Archaea possess two general transcription factors that are required to recruit RNA polymerase (RNAP) to promotersin vitro. These are TBP, the TATA-box-binding protein and TFB, the archaeal homologue of TFIIB. Thus, the archaeal and eucaryal transcription machineries are fundamentally related. In both RNAP II and archaeal transcription systems, direct contacts between TFB/TFIIB and the RNAP have been demonstrated to mediate recruitment of the polymerase to the promoter. However the subunit(s) directly contacted by these factors has not been identified. Using systematic yeast two-hybrid and bioc

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11

Wild, Gary E., Patrizia Papalia, Mark J. Ropeleski, Julio Faria, and Alan BR Thomson. "Applications of Recombinant Dna Technology in Gastrointestinal Medicine and Hepatology: Basic Paradigms of Molecular Cell Biology. Part B: Eukaryotic Gene Transcription and Post-Transcripional Rna Processing." Canadian Journal of Gastroenterology 14, no. 4 (2000): 283–92. http://dx.doi.org/10.1155/2000/385327.

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The transcription of DNA into RNA is the primary level at which gene expression is controlled in eukaryotic cells. Eukaryotic gene transcription involves several different RNA polymerases that interact with a host of transcription factors to initiate transcription. Genes that encode proteins are transcribed into messenger RNA (mRNA) by RNA polymerase II. Ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) are transcribed by RNA polymerase I and III, respectively. The production of each mRNA in human cells involves complex interactions of proteins (ie, trans-acting factors) with specific sequences

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12

Nielsen, Soren, Yulia Yuzenkova, and Nikolay Zenkin. "Mechanism of Eukaryotic RNA Polymerase III Transcription Termination." Science 340, no. 6140 (2013): 1577–80. http://dx.doi.org/10.1126/science.1237934.

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Gene expression in organisms involves many factors and is tightly controlled. Although much is known about the initial phase of transcription by RNA polymerase III (Pol III), the enzyme that synthesizes the majority of RNA molecules in eukaryotic cells, termination is poorly understood. Here, we show that the extensive structure of Pol III–synthesized transcripts dictates the release of elongation complexes at the end of genes. The poly-T termination signal, which does not cause termination in itself, causes catalytic inactivation and backtracking of Pol III, thus committing the enzyme to term

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13

Campbell, F. E., and D. R. Setzer. "Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition." Molecular and Cellular Biology 12, no. 5 (1992): 2260–72. http://dx.doi.org/10.1128/mcb.12.5.2260.

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Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is ineffi

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14

Campbell, F. E., and D. R. Setzer. "Transcription termination by RNA polymerase III: uncoupling of polymerase release from termination signal recognition." Molecular and Cellular Biology 12, no. 5 (1992): 2260–72. http://dx.doi.org/10.1128/mcb.12.5.2260-2272.1992.

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Xenopus RNA polymerase III specifically initiates transcription on poly(dC)-tailed DNA templates in the absence of other class III transcription factors normally required for transcription initiation. In experimental analyses of transcription termination using DNA fragments with a 5S rRNA gene positioned downstream of the tailed end, only 40% of the transcribing polymerase molecules terminate at the normally efficient Xenopus borealis somatic-type 5S rRNA terminators; the remaining 60% read through these signals and give rise to runoff transcripts. We find that the nascent RNA strand is ineffi

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15

Greenblatt, Jack. "RNA polymerase-associated transcription factors." Trends in Biochemical Sciences 16 (January 1991): 408–11. http://dx.doi.org/10.1016/0968-0004(91)90165-r.

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16

Ni, Zhuoyu, Abbie Saunders, Nicholas J. Fuda, et al. "P-TEFb Is Critical for the Maturation of RNA Polymerase II into Productive Elongation In Vivo." Molecular and Cellular Biology 28, no. 3 (2007): 1161–70. http://dx.doi.org/10.1128/mcb.01859-07.

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ABSTRACT Positive transcription elongation factor b (P-TEFb) is the major metazoan RNA polymerase II (Pol II) carboxyl-terminal domain (CTD) Ser2 kinase, and its activity is believed to promote productive elongation and coupled RNA processing. Here, we demonstrate that P-TEFb is critical for the transition of Pol II into a mature transcription elongation complex in vivo. Within 3 min following P-TEFb inhibition, most polymerases were restricted to within 150 bp of the transcription initiation site of the active Drosophila melanogaster Hsp70 gene, and live-cell imaging demonstrated that these p

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17

Engel, Christoph, Simon Neyer, and Patrick Cramer. "Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II." Annual Review of Biophysics 47, no. 1 (2018): 425–46. http://dx.doi.org/10.1146/annurev-biophys-070317-033058.

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RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how i

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18

Burton, Zachary F., Michael Feig, Xue Q. Gong, Chunfen Zhang, Yuri A. Nedialkov, and Yalin Xiong. "NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases." Biochemistry and Cell Biology 83, no. 4 (2005): 486–96. http://dx.doi.org/10.1139/o05-059.

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Multi-subunit RNA polymerases bind nucleotide triphosphate (NTP) substrates in the pretranslocated state and carry the dNMPNTP base pair into the active site for phosphoryl transfer. NTP-driven translocation requires that NTP substrates enter the main-enzyme channel before loading into the active site. Based on this model, a new view of fidelity and efficiency of RNA synthesis is proposed. The model predicts that, during processive elongation, NTP-driven translocation is coupled to a protein conformational change that allows pyrophosphate release: coupling the end of one bond-addition cycle t

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19

Grohmann, Dina, Angela Hirtreiter, and Finn Werner. "Molecular mechanisms of archaeal RNA polymerase." Biochemical Society Transactions 37, no. 1 (2009): 12–17. http://dx.doi.org/10.1042/bst0370012.

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All cellular life depends on multisubunit RNAPs (RNA polymerases) that are evolutionarily related through the three domains of life. Archaeal RNAPs encompass 12 subunits that contribute in different ways to the assembly and stability of the enzyme, nucleic acid binding, catalysis and specific regulatory interactions with transcription factors. The recent development of methods to reconstitute archaeal RNAP from recombinant materials in conjunction with structural information of multisubunit RNAPs present a potent opportunity to investigate the molecular mechanisms of transcription.

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20

Werner, Finn, and Robert O. J. Weinzierl. "Direct Modulation of RNA Polymerase Core Functions by Basal Transcription Factors." Molecular and Cellular Biology 25, no. 18 (2005): 8344–55. http://dx.doi.org/10.1128/mcb.25.18.8344-8355.2005.

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ABSTRACT Archaeal RNA polymerases (RNAPs) are recruited to promoters through the joint action of three basal transcription factors: TATA-binding protein, TFB (archaeal homolog of TFIIB), and TFE (archaeal homolog of TFIIE). Our results demonstrate several new insights into the mechanisms of TFB and TFE during the transcription cycle. (i) The N-terminal Zn ribbon of TFB displays a surprising degree of redundancy for the recruitment of RNAP during transcription initiation in the archaeal system. (ii) The B-finger domain of TFB participates in transcription initiation events by stimulating aborti

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21

Dorjsuren, Dorjbal, Yong Lin, Wenxiang Wei, et al. "RMP, a Novel RNA Polymerase II Subunit 5-Interacting Protein, Counteracts Transactivation by Hepatitis B Virus X Protein." Molecular and Cellular Biology 18, no. 12 (1998): 7546–55. http://dx.doi.org/10.1128/mcb.18.12.7546.

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ABSTRACT To modulate transcription, regulatory factors communicate with basal transcription factors and/or RNA polymerases in a variety of ways. Previously, it has been reported that RNA polymerase II subunit 5 (RPB5) is one of the targets of hepatitis B virus X protein (HBx) and that both HBx and RPB5 specifically interact with general transcription factor IIB (TFIIB), implying that RPB5 is one of the communicating subunits of RNA polymerase II involved in transcriptional regulation. In this context, we screened for a host protein(s) that interacts with RPB5. By far-Western blot screening, we

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22

Ruan, Jia-peng, George K. Arhin, Elisabetta Ullu, and Christian Tschudi. "Functional Characterization of a Trypanosoma brucei TATA-Binding Protein-Related Factor Points to a Universal Regulator of Transcription in Trypanosomes." Molecular and Cellular Biology 24, no. 21 (2004): 9610–18. http://dx.doi.org/10.1128/mcb.24.21.9610-9618.2004.

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ABSTRACT Transcriptional mechanisms remain poorly understood in trypanosomatid protozoa. In particular, there is no knowledge about the function of basal transcription factors, and there is an apparent rarity of promoters for protein-coding genes transcribed by RNA polymerase (Pol) II. Here we describe a Trypanosoma brucei factor related to the TATA-binding protein (TBP). Although this TBP-related factor (TBP-related factor 4 [TRF4]) has about 31% identity to the TBP core domain, several key residues involved in TATA box binding are not conserved. Depletion of the T. brucei TRF4 (TbTRF4) by RN

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Albert, Annie-Claude, Michael Denton, Milko Kermekchiev, and Craig S. Pikaard. "Histone Acetyltransferase and Protein Kinase Activities Copurify with a Putative Xenopus RNA Polymerase I Holoenzyme Self-Sufficient for Promoter-Dependent Transcription." Molecular and Cellular Biology 19, no. 1 (1999): 796–806. http://dx.doi.org/10.1128/mcb.19.1.796.

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ABSTRACT Mounting evidence suggests that eukaryotic RNA polymerases preassociate with multiple transcription factors in the absence of DNA, forming RNA polymerase holoenzyme complexes. We have purified an apparent RNA polymerase I (Pol I) holoenzyme from Xenopus laevis cells by sequential chromatography on five columns: DEAE-Sepharose, Biorex 70, Sephacryl S300, Mono Q, and DNA-cellulose. Single fractions from every column programmed accurate promoter-dependent transcription. Upon gel filtration chromatography, the Pol I holoenzyme elutes at a position overlapping the peak of Blue Dextran, sug

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Bartlett, Jon, Jelena Blagojevic, David Carter, et al. "Specialized transcription factories." Biochemical Society Symposia 73 (January 1, 2006): 67–75. http://dx.doi.org/10.1042/bss0730067.

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We have previously suggested a model for the eukaryotic genome based on the structure of the bacterial nucleoid where active RNA polymerases cluster to loop the intervening DNA. This organization of polymerases into clusters – which we call transcription ‘factories’ – has important consequences. For example, in the nucleus of a HeLa cell the concentration of soluble RNA polymerase II is ∼1 mM, but the local concentration in a factory is 1000-fold higher. Because a promoter can diffuse ∼100 nm in 15 s, one lying near a factory is likely to initiate; moreover, when released at termination, it wi

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Blombach, Fabian, Tina Daviter, Daniel Fielden, Dina Grohmann, Katherine Smollett, and Finn Werner. "Archaeology of RNA polymerase: factor swapping during the transcription cycle." Biochemical Society Transactions 41, no. 1 (2013): 362–67. http://dx.doi.org/10.1042/bst20120274.

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All RNAPs (RNA polymerases) repeatedly make use of their DNA template by progressing through the transcription cycle multiple times. During transcription initiation and elongation, distinct sets of transcription factors associate with multisubunit RNAPs and modulate their nucleic-acid-binding and catalytic properties. Between the initiation and elongation phases of the cycle, the factors have to be exchanged by a largely unknown mechanism. We have shown that the binding sites for initiation and elongation factors are overlapping and that the binding of the factors to RNAP is mutually exclusive

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Spidlova, Petra, Pavla Stojkova, Anders Sjöstedt, and Jiri Stulik. "Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors." Microorganisms 8, no. 10 (2020): 1622. http://dx.doi.org/10.3390/microorganisms8101622.

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Regulation of gene transcription is the initial step in the complex process that controls gene expression within bacteria. Transcriptional control involves the joint effort of RNA polymerases and numerous other regulatory factors. Whether global or local, positive or negative, regulators play an essential role in the bacterial cell. For instance, some regulators specifically modify the transcription of virulence genes, thereby being indispensable to pathogenic bacteria. Here, we provide a comprehensive overview of important transcription factors and DNA-binding proteins described for the virul

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Coulombe, Benoit. "DNA wrapping in transcription initiation by RNA polymerase II." Biochemistry and Cell Biology 77, no. 4 (1999): 257–64. http://dx.doi.org/10.1139/o99-028.

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The DNA wrapping model of transcription stipulates that DNA bending and wrapping around RNA polymerase causes an unwinding of the DNA helix at the enzyme catalytic center that stimulates strand separation prior to initiation and during transcript elongation. Recent experiments with mammalian RNA polymerase II indicate the significance of DNA bending and wrapping in transcriptional mechanisms. These findings have important implications in our understanding of the role of the general transcription factors in transcriptional initiation and the mechanisms underlying transcriptional regulation.Key

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Hampsey, Michael. "Molecular Genetics of the RNA Polymerase II General Transcriptional Machinery." Microbiology and Molecular Biology Reviews 62, no. 2 (1998): 465–503. http://dx.doi.org/10.1128/mmbr.62.2.465-503.1998.

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SUMMARY Transcription initiation by RNA polymerase II (RNA pol II) requires interaction between cis-acting promoter elements and trans-acting factors. The eukaryotic promoter consists of core elements, which include the TATA box and other DNA sequences that define transcription start sites, and regulatory elements, which either enhance or repress transcription in a gene-specific manner. The core promoter is the site for assembly of the transcription preinitiation complex, which includes RNA pol II and the general transcription fctors TBP, TFIIB, TFIIE, TFIIF, and TFIIH. Regulatory elements bin

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Fan, Hua-Ying, Kenneth K. Cheng та Hannah L. Klein. "Mutations in the RNA Polymerase II Transcription Machinery Suppress the Hyperrecombination Mutant hpr1 Δ of Saccharomyces cerevisiae". Genetics 142, № 3 (1996): 749–59. http://dx.doi.org/10.1093/genetics/142.3.749.

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Abstract The soh1, soh2 and soh4 mutants were isolated as suppressors of the temperature dependent growth of the hyperrecombination mutant hprl of Saccharomyces cerevisiae. Cloning and sequence analysis of these suppressor genes has unexpectedly shown them to code for components of the RNA polymerase II transcription complex. SOH2 is identical to RPB2, which encodes the second largest subunit of RNA polymerase II, and SOH4 is the same as SUA7, encoding the yeast transcription initiation factor TFIIB. SOH1 encodes a novel 14-kD protein with limited sequence similarity to RNA polymerases. Intere

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Prajapati, Ranjit K., Petja Rosenqvist, Kaisa Palmu, et al. "Oxazinomycin arrests RNA polymerase at the polythymidine sequences." Nucleic Acids Research 47, no. 19 (2019): 10296–312. http://dx.doi.org/10.1093/nar/gkz782.

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Abstract Oxazinomycin is a C-nucleoside antibiotic that is produced by Streptomyces hygroscopicus and closely resembles uridine. Here, we show that the oxazinomycin triphosphate is a good substrate for bacterial and eukaryotic RNA polymerases (RNAPs) and that a single incorporated oxazinomycin is rapidly extended by the next nucleotide. However, the incorporation of several successive oxazinomycins or a single oxazinomycin in a certain sequence context arrested a fraction of the transcribing RNAP. The addition of Gre RNA cleavage factors eliminated the transcriptional arrest at a single oxazin

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Tower, J., and B. Sollner-Webb. "Polymerase III transcription factor B activity is reduced in extracts of growth-restricted cells." Molecular and Cellular Biology 8, no. 2 (1988): 1001–5. http://dx.doi.org/10.1128/mcb.8.2.1001.

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Extracts of cells that are down-regulated for transcription by RNA polymerase I and RNA polymerase III exhibit a reduced in vitro transcriptional capacity. We have recently demonstrated that the down-regulation of polymerase I transcription in extracts of cycloheximide-treated and stationary-phase cells results from a lack of an activated subform of RNA polymerase I which is essential for rDNA transcription. To examine whether polymerase III transcriptional down-regulation occurs by a similar mechanism, the polymerase III transcription factors were isolated and added singly and in pairs to con

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Tower, J., and B. Sollner-Webb. "Polymerase III transcription factor B activity is reduced in extracts of growth-restricted cells." Molecular and Cellular Biology 8, no. 2 (1988): 1001–5. http://dx.doi.org/10.1128/mcb.8.2.1001-1005.1988.

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Extracts of cells that are down-regulated for transcription by RNA polymerase I and RNA polymerase III exhibit a reduced in vitro transcriptional capacity. We have recently demonstrated that the down-regulation of polymerase I transcription in extracts of cycloheximide-treated and stationary-phase cells results from a lack of an activated subform of RNA polymerase I which is essential for rDNA transcription. To examine whether polymerase III transcriptional down-regulation occurs by a similar mechanism, the polymerase III transcription factors were isolated and added singly and in pairs to con

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Faro-Trindade, I., and P. R. Cook. "Transcription factories: structures conserved during differentiation and evolution." Biochemical Society Transactions 34, no. 6 (2006): 1133–37. http://dx.doi.org/10.1042/bst0341133.

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Many cellular functions take place in discrete compartments, but our textbooks make little reference to any compartments involved in transcription. We review the evidence that active RNA polymerases and associated factors cluster into ‘factories’ that carry out many (perhaps all) of the functions required to generate mature transcripts. Clustering ensures high local concentrations and efficient interaction. Then, a gene must associate with the appropriate factory before it can be transcribed. Recent results show that the density and diameter of nucleoplasmic factories remain roughly constant a

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Banerjee, Rajeev, Mary K. Weidman, Sonia Navarro, Lucio Comai, and Asim Dasgupta. "Modifications of both selectivity factor and upstream binding factor contribute to poliovirus-mediated inhibition of RNA polymerase I transcription." Journal of General Virology 86, no. 8 (2005): 2315–22. http://dx.doi.org/10.1099/vir.0.80817-0.

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Soon after infection, poliovirus (PV) shuts off host-cell transcription, which is catalysed by all three cellular RNA polymerases. rRNA constitutes more than 50 % of all cellular RNA and is transcribed from rDNA by RNA polymerase I (pol I). Here, evidence has been provided suggesting that both pol I transcription factors, SL-1 (selectivity factor) and UBF (upstream binding factor), are modified and inactivated in PV-infected cells. The viral protease 3Cpro appeared to cleave the TATA-binding protein-associated factor 110 (TAF110), a subunit of the SL-1 complex, into four fragments in vitro. In

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Palmer, Adam C., J. Barry Egan, and Keith E. Shearwin. "Transcriptional interference by RNA polymerase pausing and dislodgement of transcription factors." Transcription 2, no. 1 (2011): 9–14. http://dx.doi.org/10.4161/trns.2.1.13511.

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Coulombe, Benoit, and Zachary F. Burton. "DNA Bending and Wrapping around RNA Polymerase: a “Revolutionary” Model Describing Transcriptional Mechanisms." Microbiology and Molecular Biology Reviews 63, no. 2 (1999): 457–78. http://dx.doi.org/10.1128/mmbr.63.2.457-478.1999.

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SUMMARY A model is proposed in which bending and wrapping of DNA around RNA polymerase causes untwisting of the DNA helix at the RNA polymerase catalytic center to stimulate strand separation prior to initiation. During elongation, DNA bending through the RNA polymerase active site is proposed to lower the energetic barrier to the advance of the transcription bubble. Recent experiments with mammalian RNA polymerase II along with accumulating evidence from studies of Escherichia coli RNA polymerase indicate the importance of DNA bending and wrapping in transcriptional mechanisms. The DNA-wrappi

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Brüning, Jan-Gert, and Kenneth J. Marians. "Replisome bypass of transcription complexes and R-loops." Nucleic Acids Research 48, no. 18 (2020): 10353–67. http://dx.doi.org/10.1093/nar/gkaa741.

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Abstract The vast majority of the genome is transcribed by RNA polymerases. G+C-rich regions of the chromosomes and negative superhelicity can promote the invasion of the DNA by RNA to form R-loops, which have been shown to block DNA replication and promote genome instability. However, it is unclear whether the R-loops themselves are sufficient to cause this instability or if additional factors are required. We have investigated replisome collisions with transcription complexes and R-loops using a reconstituted bacterial DNA replication system. RNA polymerase transcription complexes co-directi

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Kassavetis, G. A., and E. P. Geiduschek. "Transcription factor TFIIIB and transcription by RNA polymerase III." Biochemical Society Transactions 34, no. 6 (2006): 1082–87. http://dx.doi.org/10.1042/bst0341082.

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pol (RNA polymerase) III is charged with the task of transcribing nuclear genes encoding diverse small structural and catalytic RNAs. We present a brief review of the current understanding of several aspects of the pol III transcription apparatus. The focus is on yeast and, more specifically, on Saccharomyces cerevisiae; preponderant attention is given to the TFs (transcription initiation factors) and especially to TFIIIB, which is the core pol III initiation factor by virtue of its role in recruiting pol III to the transcriptional start site and its essential roles in forming the transcriptio

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39

Orphanides, G., T. Lagrange, and D. Reinberg. "The general transcription factors of RNA polymerase II." Genes & Development 10, no. 21 (1996): 2657–83. http://dx.doi.org/10.1101/gad.10.21.2657.

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40

Sawadogo, M., and A. Sentenac. "RNA Polymerase B (II) and General Transcription Factors." Annual Review of Biochemistry 59, no. 1 (1990): 711–54. http://dx.doi.org/10.1146/annurev.bi.59.070190.003431.

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Gabrielsen, Odd S., and Andre´ Sentenac. "RNA polymerase III (C) and its transcription factors." Trends in Biochemical Sciences 16 (January 1991): 412–16. http://dx.doi.org/10.1016/0968-0004(91)90166-s.

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42

Knutson, Bruce A., and Steven Hahn. "TFIIB-related factors in RNA polymerase I transcription." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1829, no. 3-4 (2013): 265–73. http://dx.doi.org/10.1016/j.bbagrm.2012.08.003.

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43

Acker, Joël, Christine Conesa, and Olivier Lefebvre. "Yeast RNA polymerase III transcription factors and effectors." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1829, no. 3-4 (2013): 283–95. http://dx.doi.org/10.1016/j.bbagrm.2012.10.002.

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44

Panov, Kostya I., Tatiana B. Panova, Olivier Gadal, et al. "RNA Polymerase I-Specific Subunit CAST/hPAF49 Has aRole in the Activation of Transcription by UpstreamBinding Factor." Molecular and Cellular Biology 26, no. 14 (2006): 5436–48. http://dx.doi.org/10.1128/mcb.00230-06.

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ABSTRACT Eukaryotic RNA polymerases are large complexes, 12 subunits of which are structurally or functionally homologous across the three polymerase classes. Each class has a set of specific subunits, likely targets of their cognate transcription factors. We have identified and characterized a human RNA polymerase I (Pol I)-specific subunit, previously identified as ASE-1 (antisense of ERCC1) and as CD3ε-associated signal transducer (CAST), and here termed CAST or human Pol I-associated factor of 49 kDa (hPAF49), after mouse orthologue PAF49. We provide evidence for growth-regulated Tyr phosp

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Zenkin, Nikolay. "Multiple personalities of the RNA polymerase active centre." Microbiology 160, no. 7 (2014): 1316–20. http://dx.doi.org/10.1099/mic.0.079020-0.

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Transcription in all living organisms is accomplished by highly conserved multi-subunit RNA polymerases (RNAPs). Our understanding of the functioning of the active centre of RNAPs has transformed recently with the finding that a conserved flexible domain near the active centre, the trigger loop (TL), participates directly in the catalysis of RNA synthesis and serves as a major determinant for fidelity of transcription. It also appears that the TL is involved in the unique ability of RNAPs to exchange catalytic activities of the active centre. In this phenomenon the TL is replaced by a transcri

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Artsimovitch, Irina, Vladimir Svetlov, Larry Anthony, Richard R. Burgess, and Robert Landick. "RNA Polymerases from Bacillus subtilisand Escherichia coli Differ in Recognition of Regulatory Signals In Vitro." Journal of Bacteriology 182, no. 21 (2000): 6027–35. http://dx.doi.org/10.1128/jb.182.21.6027-6035.2000.

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ABSTRACT Adaptation of bacterial cells to diverse habitats relies on the ability of RNA polymerase to respond to various regulatory signals. Some of these signals are conserved throughout evolution, whereas others are species specific. In this study we present a comprehensive comparative analysis of RNA polymerases from two distantly related bacterial species, Escherichia coli and Bacillus subtilis, using a panel of in vitro transcription assays. We found substantial species-specific differences in the ability of these enzymes to escape from the promoter and to recognize certain types of elong

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Zawel, L., K. P. Kumar, and D. Reinberg. "Recycling of the general transcription factors during RNA polymerase II transcription." Genes & Development 9, no. 12 (1995): 1479–90. http://dx.doi.org/10.1101/gad.9.12.1479.

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Roussel, P., C. André, L. Comai, and D. Hernandez-Verdun. "The rDNA transcription machinery is assembled during mitosis in active NORs and absent in inactive NORs." Journal of Cell Biology 133, no. 2 (1996): 235–46. http://dx.doi.org/10.1083/jcb.133.2.235.

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In cycling cells, the rDNAs are expressed from telophase to the end of G2 phase. The early resumption of rDNA transcription at telophase raises the question of the fate of the rDNA transcription machinery during mitosis. At the beginning of mitosis, rDNA transcription is arrested, and the rDNAs are clustered in specific chromosomal sites, the nucleolar organizer regions (NOR). In human cells, we demonstrate that the rDNA transcription machinery, as defined in vitro, is colocalized in some NORs and absent from others whatever the mitotic phase: RNA polymerase I and the RNA polymerase I transcri

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Damania, Blossom, Renu Mital, and James C. Alwine. "Simian Virus 40 Large T Antigen Interacts with Human TFIIB-Related Factor and Small Nuclear RNA-Activating Protein Complex for Transcriptional Activation of TATA-Containing Polymerase III Promoters." Molecular and Cellular Biology 18, no. 3 (1998): 1331–38. http://dx.doi.org/10.1128/mcb.18.3.1331.

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ABSTRACTThe TATA-binding protein (TBP) is common to the basal transcription factors of all three RNA polymerases, being associated with polymerase-specific TBP-associated factors (TAFs). Simian virus 40 large T antigen has previously been shown to interact with the TBP-TAFII complexes, TFIID (B. Damania and J. C. Alwine, Genes Dev. 10:1369–1381, 1996), and the TBP-TAFIcomplex, SL1 (W. Zhai, J. Tuan, and L. Comai, Genes Dev. 11:1605–1617, 1997), and in both cases these interactions are critical for transcriptional activation. We show a similar mechanism for activation of the class 3 polymerase

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Zhang, Yuli, and Linlin Hou. "Alternate Roles of Sox Transcription Factors beyond Transcription Initiation." International Journal of Molecular Sciences 22, no. 11 (2021): 5949. http://dx.doi.org/10.3390/ijms22115949.

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Sox proteins are known as crucial transcription factors for many developmental processes and for a wide range of common diseases. They were believed to specifically bind and bend DNA with other transcription factors and elicit transcriptional activation or repression activities in the early stage of transcription. However, their functions are not limited to transcription initiation. It has been showed that Sox proteins are involved in the regulation of alternative splicing regulatory networks and translational control. In this review, we discuss the current knowledge on how Sox transcription f

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