101
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Ljungman M, O'Hagan HM, Paulsen MT. Induction of ser15 and lys382 modifications of p53 by blockage of transcription elongation. Oncogene 2001; 20:5964-71. [PMID: 11593403 DOI: 10.1038/sj.onc.1204734] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2001] [Revised: 06/07/2001] [Accepted: 06/14/2001] [Indexed: 11/09/2022]
Abstract
Blockage of transcription has been shown to induce the tumor suppressor p53 in human cells. We here show that RNA synthesis inhibitors blocking the phosphorylation of the carboxyl terminal domain (CTD) of RNA polymerase II, such as DRB and H7, induced rapid nuclear accumulation of p53 proteins that were not phosphorylated at ser15 or acetylated at lys382. In contrast, agents that inhibit the elongation phase of transcription, such as UV light, camptothecin or actinomycin D, induced the accumulation of nuclear p53 proteins that were modified at both of these sites. Furthermore, using a panel of DNA repair-deficient cells we show that persistent DNA lesions in the transcribed strand of active genes are responsible for the induction of the ser15 and lys382 modifications following UV-irradiation. We conclude that inhibition of transcription is sufficient for the accumulation of p53 in the nucleus regardless of whether the ser15 site of p53 is phosphorylated or not. Importantly, blockage of the elongation phase of transcription triggers a distinct signaling pathway leading to p53 modifications on ser15 and lys382. We propose that the elongating RNA polymerase complex may act as a sensor of DNA damage and as an integrator of cellular stress signals.
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Affiliation(s)
- M Ljungman
- Department of Radiation Oncology, Division of Cancer Biology, University of Michigan Comprehensive Cancer Center, 150 E. Medical Center Drive, Ann Arbor, MI 48109-0936, USA.
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102
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Sato S, Wong SK, Lazinski DW. Hepatitis delta virus minimal substrates competent for editing by ADAR1 and ADAR2. J Virol 2001; 75:8547-55. [PMID: 11507200 PMCID: PMC115100 DOI: 10.1128/jvi.75.18.8547-8555.2001] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A host-mediated RNA-editing event allows hepatitis delta virus (HDV) to express two essential proteins, the small delta antigen (HDAg-S) and the large delta antigen (HDAg-L), from a single open reading frame. One or several members of the ADAR (adenosine deaminases that act on RNA) family are thought to convert the adenosine to an inosine (I) within the HDAg-S amber codon in antigenomic RNA. As a consequence of replication, the UIG codon is converted to a UGG (tryptophan [W]) codon in the resulting HDAg-L message. Here, we used a novel reporter system to monitor the editing of the HDV amber/W site in the absence of replication. In cultured cells, we observed that both human ADAR1 (hADAR1) and hADAR2 were capable of editing the amber/W site with comparable efficiencies. We also defined the minimal HDV substrate required for hADAR1- and hADAR2-mediated editing. Only 24 nucleotides from the amber/W site were sufficient to enable efficient editing by hADAR1. Hence, the HDV amber/W site represents the smallest ADAR substrate yet identified. In contrast, the minimal substrate competent for hADAR2-mediated editing contained 66 nucleotides.
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Affiliation(s)
- S Sato
- Department of Molecular Biology and Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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103
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Terhune SS, Hubert WG, Thomas JT, Laimins LA. Early polyadenylation signals of human papillomavirus type 31 negatively regulate capsid gene expression. J Virol 2001; 75:8147-57. [PMID: 11483760 PMCID: PMC115059 DOI: 10.1128/jvi.75.17.8147-8157.2001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The L1 and L2 capsid genes of human papillomavirus type 31 (HPV-31) are expressed upon keratinocyte differentiation from a promoter located in the E7 open reading frame (ORF) of the early region. Late transcripts must therefore pass through and ignore the early polyadenylation sequences to use the downstream late AAUAAA element located at the end of the L1 ORF. To identify sequences which modulate downstream capsid gene expression, a variety of substitution mutations were introduced into the early polyadenylation signal and studied first in the context of polycistronic luciferase reporter constructs. Removal of the G/U-rich cleavage stimulation factor (CstF) binding sites and the degenerate cleavage and polyadenylation specificity factor binding sites, UAUAUA, had minimal effect on downstream expression as defined by luciferase activities. This is in contrast to the deletion of the HPV-31 early AAUAAA element, which resulted in a dramatic increase in downstream expression. Additional sequences within the first 800 bp of the L2 ORF were also found to negatively regulate capsid expression in luciferase assays. To determine how these mutations influence gene expression in the context of the complete HPV-31 genome, recombinant genomes were constructed that contained a substitution in the AAUAAA sequence, an inserted strong CstF binding site, an inserted simian virus 40 (SV40) late poly(A) signal, or a substitution of the 5'-most 800 nucleotides of the L2 ORF. Reductions in both transient and stable replication were observed with the recombinant genomes containing the strong CstF site or the late SV40 signal, suggesting that alterations in the strength of the upstream poly(A) signal influence expression of viral replication factors. Similarly, disruption of the L2 ORF resulted in a significant reduction in genome replication and an inability to be maintained stably. In contrast, genomes containing a substitution of the AAUAAA sequence had increased levels of transient and stable replication. Quantitation of late transcripts following keratinocyte differentiation in methylcellulose also showed a reduction in downstream capsid gene expression in lines containing genomes with the strong CstF site or the late SV40 signal mutations, while a significant increase in expression was detected in the lines with genomes lacking the AAUAAA sequence. These studies demonstrate that capsid gene expression in HPV-31 requires an inefficient early poly(A) signal which is defined primarily by the AAUAAA element as well as a major negative regulatory element located within the L2 ORF.
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Affiliation(s)
- S S Terhune
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois 606113, USA
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104
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Abstract
As in other eucaryotes, the nuclear genome in Trypanosoma brucei is organised into silent domains and active domains transcribed by distinct RNA polymerases. The basic mechanisms underlying eucaryotic gene transcription are conserved between humans and yeast, and understood in some detail in these cells. Meanwhile, relatively little is known about the transcription machinery, the chromatin templates or their interactions in trypanosomatids. Here, I discuss and compare nuclear gene transcription in T. brucei with transcription in other eucaryotes focusing in particular on mono-allelic transcription of genes that encode the variant surface glycoproteins.
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Affiliation(s)
- D Horn
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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105
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Awasthi S, Palmer R, Castro M, Mobarak CD, Ruby SW. New roles for the Snp1 and Exo84 proteins in yeast pre-mRNA splicing. J Biol Chem 2001; 276:31004-15. [PMID: 11425851 DOI: 10.1074/jbc.m100022200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian 70K protein, a component of the U1 small nuclear ribonucleoprotein involved in pre-mRNA splicing, interacts with a number of proteins important for regulating constitutive and alternative splicing. Similar proteins that interact with the yeast homolog of the 70K protein, Snp1p, have yet to be identified. We used the two-hybrid system to find four U1-Snp1 associating (Usa) proteins. Two of these proteins physically associate with Snp1p as assayed by coimmunoprecipitation. One is Prp8p, a known, essential spliceosomal component. This interaction suggests some novel functions for Snp1p and the U1 small nuclear ribonucleoprotein late in spliceosome development. The other, Exo84p, is a conserved subunit of the exocyst, an eight-protein complex functioning in secretion. We show here that Exo84p is also involved in pre-mRNA splicing. A temperature-sensitive exo84 mutation caused increased ratios of pre-mRNA to mRNA for the Rpl30 and actin transcripts in cells incubated at the non-permissive temperature. The mutation also led to a defect in splicing and prespliceosome formation in vitro; an indication that Exo84p has a direct role in splicing. The results elucidate a surprising link between splicing and secretion.
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Affiliation(s)
- S Awasthi
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Cancer Research and Treatment Center, Albuquerque, New Mexico 87131, USA
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106
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Ochotorena IL, Hirata D, Kominami K, Potashkin J, Sahin F, Wentz-Hunter K, Gould KL, Sato K, Yoshida Y, Vardy L, Toda T. Conserved Wat1/Pop3 WD-repeat protein of fission yeast secures genome stability through microtubule integrity and may be involved in mRNA maturation. J Cell Sci 2001; 114:2911-20. [PMID: 11686295 DOI: 10.1242/jcs.114.16.2911] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate chromosome segregation is dependent upon the integrity of mitotic spindles, which pull each pair of sister chromatids towards opposite poles. In this study, we have characterised fission yeast pop3-5235, a diploidising mutant that is impaired in genome stability. Pop3 is the same as Wat1, a conserved protein containing 7 WD repeats. Pop3/Wat1 has also been isolated from a two-hybrid screen as a binding partner to Prp2, the large subunit of the essential splicing factor U2AF. In wat1 mutants, the cellular amount of α-tubulin is decreased to very low levels, which results in compromised microtubules and spindles, consequently leading to unequal chromosome separation. Further analysis shows that, in spite of the binding between Wat1 and Prp2, Wat1 may not be involved directly in splicing reactions per se. Instead, we find that Wat1 is required for the maintenance of α-tubulin mRNA levels; moreover, transcript levels of genes other than the α-tubulin gene are also equally decreased in this mutant. Wild-type Wat1, but not the mutant protein, forms a large complex in the cell with several other proteins, suggesting that Wat1 functions as a structural linker in the complex. The results suggest that Wat1 plays a role in mRNA maturation as a coupling protein between splicing and synthesis and/or stabilisation.
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Affiliation(s)
- I L Ochotorena
- Laboratory of Cell Regulation, Imperial Cancer Research Fund, London, UK
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107
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Abstract
Proteins are responsible for most cellular and extra-cellular functions. If altered, proteins can loose their normal activity and/or gain new properties. Either way the consequences may be deleterious for the cell and lead to disease at the organism level. Not surprisingly, eukaryotes have evolved mechanisms to recognize abnormal messenger RNAs and prevent them from producing faulty proteins. Protein-encoding genes are transcribed in the nucleus by RNA polymerase II as precursor RNAs that undergo extensive processing before being translocated to the cytoplasm for translation by the ribosomes. This spatial and temporal separation between RNA and protein synthesis offers an immense opportunity for control and regulation. Here we review recent studies that are beginning to unravel how the coupling between transcription, processing and transport of mRNAs contributes to control the quality of gene expression in the nucleus.
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Affiliation(s)
- N Custódio
- Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
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108
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Cramer P, Srebrow A, Kadener S, Werbajh S, de la Mata M, Melen G, Nogués G, Kornblihtt AR. Coordination between transcription and pre-mRNA processing. FEBS Lett 2001; 498:179-82. [PMID: 11412852 DOI: 10.1016/s0014-5793(01)02485-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A large body of work has proved that transcription by RNA polymerase II and pre-mRNA processing are coordinated events within the cell nucleus. Capping, splicing and polyadenylation occur while transcription proceeds, suggesting that RNA polymerase II plays a role in the regulation of these events. The presence and degree of phosphorylation of the carboxy-terminal domain of RNA polymerase II large subunit is important for functioning of the capping enzymes, the assembly of spliceosomes and the binding of the cleavage/polyadenylation complex. Nuclear architecture and gene promoter structure have also been shown to play key roles in coupling between transcription and splicing.
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Affiliation(s)
- P Cramer
- Laboratorio de Fisiología y Biología Molecular, Departamento de Ciencias Biológicas, Universidad de Buenos Aires, Ciudad Universitaria, Argentina
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109
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Cramer P, Bushnell DA, Kornberg RD. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 2001; 292:1863-76. [PMID: 11313498 DOI: 10.1126/science.1059493] [Citation(s) in RCA: 934] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Structures of a 10-subunit yeast RNA polymerase II have been derived from two crystal forms at 2.8 and 3.1 angstrom resolution. Comparison of the structures reveals a division of the polymerase into four mobile modules, including a clamp, shown previously to swing over the active center. In the 2.8 angstrom structure, the clamp is in an open state, allowing entry of straight promoter DNA for the initiation of transcription. Three loops extending from the clamp may play roles in RNA unwinding and DNA rewinding during transcription. A 2.8 angstrom difference Fourier map reveals two metal ions at the active site, one persistently bound and the other possibly exchangeable during RNA synthesis. The results also provide evidence for RNA exit in the vicinity of the carboxyl-terminal repeat domain, coupling synthesis to RNA processing by enzymes bound to this domain.
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MESH Headings
- Amino Acid Sequence
- Binding Sites
- Conserved Sequence
- Crystallography, X-Ray
- DNA, Fungal/chemistry
- DNA, Fungal/metabolism
- Fourier Analysis
- Hydrogen Bonding
- Magnesium/metabolism
- Metals/metabolism
- Models, Molecular
- Molecular Sequence Data
- Promoter Regions, Genetic
- Protein Conformation
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Subunits
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Fungal/biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- P Cramer
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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110
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Dye MJ, Proudfoot NJ. Multiple transcript cleavage precedes polymerase release in termination by RNA polymerase II. Cell 2001; 105:669-81. [PMID: 11389836 DOI: 10.1016/s0092-8674(01)00372-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The requirement of poly(A) signals to elicit transcription termination of RNA polymerase II (pol II) is firmly established. However, little else is known about the actual process of pol II transcription termination. Evidence presented in this paper, based on analysis of nascent transcripts of the human beta- and epsilon-globin genes, demonstrates that pol II transcription termination involves two distinct and temporally separate events. The first event, termed pretermination cleavage (PTC), is mediated by sequence tracts located downstream of the poly(A) site which appear to promote heterogeneous cleavage of the nascent transcript. The second event, in which pol II disengages from the DNA template, requires that polymerase has transcribed both a PTC sequence tract and a functional poly(A) site.
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Affiliation(s)
- M J Dye
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
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111
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Calvo O, Manley JL. Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination. Mol Cell 2001; 7:1013-23. [PMID: 11389848 DOI: 10.1016/s1097-2765(01)00236-2] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Tight connections exist between transcription and subsequent processing of mRNA precursors, and interactions between the transcription and polyadenylation machineries seem especially extensive. Using a yeast two-hybrid screen to identify factors that interact with the polyadenylation factor CstF-64, we uncovered an interaction with the transcriptional coactivator PC4. Both human proteins have yeast homologs, Rna15p and Sub1p, respectively, and we show that these two proteins also interact. Given evidence that certain polyadenylation factors, including Rna15p, are necessary for termination in yeast, we show that deletion or overexpression of SUB1 suppresses or enhances, respectively, both growth and termination defects detected in an rna15 mutant strain. Our findings provide an additional, unexpected connection between transcription and polyadenylation and suggest that PC4/Sub1p, via its interaction with CstF-64/Rna15p, possesses an evolutionarily conserved antitermination activity.
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Affiliation(s)
- O Calvo
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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112
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Abstract
The levels of cellular messenger RNA transcripts can be regulated by controlling the rate at which the mRNA decays. Because decay rates affect the expression of specific genes, they provide a cell with flexibility in effecting rapid change. Moreover, many clinically relevant mRNAs--including several encoding cytokines, growth factors and proto-oncogenes--are regulated by differential RNA stability. But what are the sequence elements and factors that control the half-lives of mRNAs?
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Affiliation(s)
- C J Wilusz
- Department of Molecular Genetics and Microbiology, Robert Wood Johnson Medical School-UMDNJ, Piscataway, New Jersey 08854, USA
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113
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Stoss O, Olbrich M, Hartmann AM, Konig H, Memmott J, Andreadis A, Stamm S. The STAR/GSG family protein rSLM-2 regulates the selection of alternative splice sites. J Biol Chem 2001; 276:8665-73. [PMID: 11118435 DOI: 10.1074/jbc.m006851200] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We identified the rat Sam68-like mammalian protein (rSLM-2), a member of the STAR (signal transduction and activation of RNA) protein family as a novel splicing regulatory protein. Using the yeast two-hybrid system, coimmunoprecipitations, and pull-down assays, we demonstrate that rSLM-2 interacts with various proteins involved in the regulation of alternative splicing, among them the serine/arginine-rich protein SRp30c, the splicing-associated factor YT521-B and the scaffold attachment factor B. rSLM-2 can influence the splicing pattern of the CD44v5, human transformer-2beta and tau minigenes in cotransfection experiments. This effect can be reversed by rSLM-2-interacting proteins. Employing rSLM-2 deletion variants, gel mobility shift assays, and linker scan mutations of the CD44 minigene, we show that the rSLM-2-dependent inclusion of exon v5 of the CD44 pre-mRNA is dependent on a short purine-rich sequence. Because the related protein of rSLM-2, Sam68, is believed to play a role as an adapter protein during signal transduction, we postulate that rSLM-2 is a link between signal transduction pathways and pre-mRNA processing.
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Affiliation(s)
- O Stoss
- Max-Planck Institute of Neurobiology, Am Klopferspitz 18a, D-82152 Martinsried, the Forschungszentrum Karlsruhe, Institut für Genetik, Postfach 3640, D-76021 Karlsruhe, Germany
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114
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Reynaud CA, Frey S, Aoufouchi S, Faili A, Bertocci B, Dahan A, Flatter E, Delbos F, Storck S, Zober C, Weill JC. Transcription, beta-like DNA polymerases and hypermutation. Philos Trans R Soc Lond B Biol Sci 2001; 356:91-7. [PMID: 11205336 PMCID: PMC1087696 DOI: 10.1098/rstb.2000.0753] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This paper discusses two aspects of immunoglobulin (Ig) gene hypermutation. In the first approach, a transcription termination signal is introduced in an Ig light chain transgene acting as a mutation substrate, and transgenic lines are generated with control and mutant transgenes integrated in tandem. Analysis of transcription levels and mutation frequencies between mutant and control transgenes clearly dissociates transcription elongation and mutation, and therefore argues against models whereby specific pausing of the RNA polymerase during V gene transcription would trigger an error-prone repair process. The second part reports the identification of two novel beta-like DNA polymerases named Pol lambda and Pol mu, one of which (Pol mu) represents a good candidate for the Ig mutase due to its higher lymphoid expression and its similarity with the lymphoid enzyme terminal deoxynucleotidyl transferase. Peculiar features of the expression of this gene, including an unusual splicing variability and a splicing inhibition in response to DNA-damaging agents, are discussed.
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Affiliation(s)
- C A Reynaud
- Institut National de la Santé et de la Recherche Médicale U373, Faculté de Médecine Necker-Enfants Malades, Université Paris V, France.
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115
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Affiliation(s)
- L E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.
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116
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Chan JY, Lee-Prudhoe JE, Jorgensen B, Ihrke G, Doyonnas R, Zannettino AC, Buckle VJ, Ward CJ, Simmons PJ, Watt SM. Relationship between novel isoforms, functionally important domains, and subcellular distribution of CD164/endolyn. J Biol Chem 2001; 276:2139-52. [PMID: 11027692 DOI: 10.1074/jbc.m007965200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Functional analyses have indicated that the human CD164 sialomucin may play a key role in hematopoiesis by facilitating the adhesion of human CD34(+) cells to the stroma and by negatively regulating CD34(+)CD38(lo/-) cell proliferation. We have identified three novel human CD164 variants derived by alternative splicing of bona fide exons from a single genomic transcription unit. The predominant CD164(E1-6) isoform, encoded by six exons, is a type I transmembrane protein containing two extracellular mucin domains (I and II) interrupted by a cysteine-rich non-mucin domain. The 103B2/9E10 and 105A5 epitopes, which specify ligand binding characteristics, are located on the exon 1-encoded mucin domain I. Three human CD164(E1-6) mRNA species, exhibiting differential polyadenylation site usage, are differentially expressed in hematopoietic and non-hematopoietic tissues. This study provides additional evidence that human CD164(E1-6) represents the ortholog of murine MGC-24v and rat endolyn. Comparative analysis of murine MGC-24v/CD164(E1-6) with human CD164(E1-6) revealed two potential splice variants and a similar genomic structure. Whereas the human CD164 gene is located on chromosome 6q21, the mouse gene occurs in a syntenic region on chromosome 10B1-B2. By confocal microscopy, human CD164 in CD34(+)CD38(+) hematopoietic progenitor (KG1B) and epithelial cell lines appears to be localized primarily in endosomes and lysosomes, with low concentrations at the cell surface. However, in a minority of KG1B cells, CD164 is more prominently expressed at the plasma membrane and in the recycling endosomes, suggesting that its distribution is regulated in cells of hematopoietic origin.
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Affiliation(s)
- J Y Chan
- Medical Research Council Molecular Hematology Unit, Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
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117
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Barillà D, Lee BA, Proudfoot NJ. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2001; 98:445-50. [PMID: 11149954 PMCID: PMC14606 DOI: 10.1073/pnas.98.2.445] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II plays an important role in transcription and processing of the nascent transcript by interacting with both transcription and RNA processing factors. We show here that the cleavage/polyadenylation factor IA of Saccharomyces cerevisiae directly contacts CTD. First by affinity chromatography experiments with yeast extracts we demonstrate that the Rna15p, Rna14p, and Pcf11p subunits of this complex are associated with phosphorylated CTD. This interaction is confirmed for Rna15p by yeast two-hybrid analysis. Second, Pcf11p, but not Rna15p, is shown to directly contact phosphorylated CTD based on in vitro binding studies with recombinant proteins. These findings establish a direct interaction of cleavage/polyadenylation factor IA with the CTD. Furthermore, a quantitative analysis of transcription run-on performed on temperature-sensitive mutant strains reveals that the lack of either functional Rna14p or Pcf11p affects transcription termination more severely than the absence of a functional Rna15p. Moreover, these data reinforce the concept that CTD phosphorylation acts as a regulatory mechanism in the maturation of the primary transcript.
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Affiliation(s)
- D Barillà
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
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118
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Gallardo M, Aguilera A. A new hyperrecombination mutation identifies a novel yeast gene, THP1, connecting transcription elongation with mitotic recombination. Genetics 2001; 157:79-89. [PMID: 11139493 PMCID: PMC1461480 DOI: 10.1093/genetics/157.1.79] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Given the importance of the incidence of recombination in genomic instability, it is of great interest to know the elements or processes controlling recombination in mitosis. One such process is transcription, which has been shown to induce recombination in bacteria, yeast, and mammals. To further investigate the genetic control of the incidence of recombination and genetic instability and, in particular, its connection with transcription, we have undertaken a search for hyperrecombination mutants among a large number of strains deleted in genes of unknown function. We have identified a new gene, THP1 (YOL072w), whose deletion mutation strongly stimulates recombination between repeats. In addition, thp1 Delta impairs transcription, a defect that is particularly strong at the level of elongation through particular DNA sequences such as lacZ. The hyperrecombination phenotype of thp1 Delta cells is fully dependent on transcription elongation of the repeat construct. When transcription is impeded either by shutting off the promoter or by using a premature transcription terminator, hyperrecombination between repeats is abolished, providing new evidence that transcription-elongation impairment may be a source of recombinogenic substrates in mitosis. We show that Thp1p and two other proteins previously shown to control transcription-associated recombination, Hpr1p and Tho2p, act in the same "pathway" connecting transcription elongation with the incidence of mitotic recombination.
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Affiliation(s)
- M Gallardo
- Departamento de Genética, Universidad de Sevilla, 41012 Seville, Spain
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119
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The Transcription of Genes. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50031-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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120
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Fodor E, Mikulasova A, Mingay LJ, Poon LL, Brownlee GG. Messenger RNAs that are not synthesized by RNA polymerase II can be 3' end cleaved and polyadenylated. EMBO Rep 2000; 1:513-8. [PMID: 11263496 PMCID: PMC1083783 DOI: 10.1093/embo-reports/kvd111] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The poly(A) tail of influenza virus mRNAs is synthesized by the viral RNA polymerase by reiterative copying of a U5-7 sequence near the 5' end of the viral RNA (vRNA) template. We have engineered a vRNA molecule by replacing its viral U6 poly(A) site with a negative-sense eukaryotic polyadenylation signal. The vRNA was transcribed by the viral RNA polymerase and the transcription product was processed by the cellular 3' end processing machinery in vivo. According to the current model, 3' end processing of eukaryotic pre-mRNAs is coupled to cellular RNA polymerase II (pol II) transcription; thus only RNAs synthesized by pol III are believed to be polyadenylated efficiently. Our results show that the cellular polyadenylation machinery is nevertheless able to recognize and process RNA transcripts that are not synthesized by pol II, indicating that synthesis by pol II is not an absolute requirement for 3' end processing in vivo.
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Affiliation(s)
- E Fodor
- Sir William Dunn School of Pathology, University of Oxford, UK
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Fritz DT, Ford LP, Wilusz J. An in vitro assay to study regulated mRNA stability. SCIENCE'S STKE : SIGNAL TRANSDUCTION KNOWLEDGE ENVIRONMENT 2000; 2000:pl1. [PMID: 11752625 DOI: 10.1126/stke.2000.61.pl1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The examination of posttranscriptional regulation of mRNA in mammalian cells is critical to discovering the role that mRNA plays in the initiation and maintenance of cellular processes. The complexity of the system defies a holistic approach and, therefore, we have devised an in vitro mRNA turnover assay that enables us to elucidate the factors involved in mRNA deadenylation and degradation. Our system, using an S100 HeLa extract and in vitro transcribed RNAs, accurately mimics the end products of mRNA turnover, which have been previously described using in vivo studies and, in addition, allows for the detailed study of factors that may play a role in regulated deadenylation and degradation. Another important aspect of our system is the ease with which it can be manipulated. We can provide any synthetic RNA molecule to the assay to test for specific sequence activity. Furthermore, the results are clear and accurately interpretable. We have demonstrated that our in vitro system accurately deadenylates and decays a capped and polyadenylated RNA molecule in a processive manner without nonspecific nuclease activity. Finally, we have demonstrated regulated instability in vitro using the AU-rich elements (AREs) from tumor necrosis factor-alpha (TNF-alpha) and granulocyte macrophage colony stimulating factor (GM-CSF) embedded within the RNA molecule. The presence of the AREs increased the deadenylation and the decay rates seen in vivo. We feel that this system can be expanded and adapted to examine a variety of mRNA regulatory events in mammalian cells.
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Affiliation(s)
- D T Fritz
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
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Fritz DT, Ford LP, Wilusz J. An in Vitro Assay to Study Regulated mRNA Stability. Sci Signal 2000. [DOI: 10.1126/scisignal.612000pl1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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de Vries H, Rüegsegger U, Hübner W, Friedlein A, Langen H, Keller W. Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors. EMBO J 2000; 19:5895-904. [PMID: 11060040 PMCID: PMC305781 DOI: 10.1093/emboj/19.21.5895] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Six different protein factors are required in vitro for 3' end formation of mammalian pre-mRNAs by endonucleolytic cleavage and polyadenylation. Five of the factors have been purified and most of their components cloned, but cleavage factor II(m) (CF II(m)) remained uncharacterized. We have purified CF II(m) from HeLa cell nuclear extract by several chromatographic steps. During purification, CF II(m) activity separated into two components, one essential (CF IIA(m)) and one stimulatory (CF IIB(m)) for the cleavage reaction. CF IIA(m) fractions contain the human homologs of two yeast 3' end processing factors, Pcf11p and Clp1p, as well as cleavage factor I(m) (CF I(m)) and several splicing and transcription factors. We report the cloning of hClp1 and show that it is a genuine subunit of CF IIA(m). Antibodies directed against hClp1 deplete cleavage activity, but not polyadenylation activity from HeLa cell nuclear extract. hClp1 interacts with CF I(m) and the cleavage and polyadenylation specificity factor CPSF, suggesting that it bridges these two 3' end processing factors within the cleavage complex.
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Affiliation(s)
- H de Vries
- Department of Cell Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Germany
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Comer FI, Hart GW. O-Glycosylation of nuclear and cytosolic proteins. Dynamic interplay between O-GlcNAc and O-phosphate. J Biol Chem 2000; 275:29179-82. [PMID: 10924527 DOI: 10.1074/jbc.r000010200] [Citation(s) in RCA: 283] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- F I Comer
- Graduate Program, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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