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Yalamanchili P, Weidman K, Dasgupta A. Cleavage of transcriptional activator Oct-1 by poliovirus encoded protease 3Cpro. Virology 1997; 239:176-85. [PMID: 9426457 DOI: 10.1006/viro.1997.8862] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In HeLa cells, RNA polymerase II mediated transcription is severely inhibited by poliovirus infection. Both basal and activated transcription are affected to bring about a complete shutoff of host cell transcription. We demonstrate here that the octamer binding transcription factor, Oct-1, is cleaved in HeLa cells infected with poliovirus. Incubation of Oct-1 with the purified, recombinant 3Cpro results in the generation of the cleaved Oct-1 product seen in virus infected cells. Poliovirus infection leads to the formation of altered Oct-1 DNA complexes that can also be generated by incubation of Oct-1 with purified 3Cpro. We also show that Oct-1 cleaved by 3Cpro loses its ability to inhibit transcriptional activation by the SV40 B enhancer. These results suggest that cleavage of Oct-1 in poliovirus infected cells leads to the loss of its activity.
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Affiliation(s)
- P Yalamanchili
- Department of Microbiology and Immunology, UCLA School of Medicine 90095-1747, USA
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2
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Huang L, Zhu Y, Anders DG. The variable 3' ends of a human cytomegalovirus oriLyt transcript (SRT) overlap an essential, conserved replicator element. J Virol 1996; 70:5272-81. [PMID: 8764037 PMCID: PMC190484 DOI: 10.1128/jvi.70.8.5272-5281.1996] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The genetically defined human cytomegalovirus (HCMV) lytic-phase replicator, oriLyt, comprises more than 2 kb in a structurally complex region that spans a variety of potential transcription control signals. Several transcripts originate within or cross oriLyt, and we are studying these oriLyt transcription units to determine whether they participate in initiating or regulating lytic-phase DNA synthesis. Results presented here establish the temporal accumulation and structure of the smallest replicator transcript, which we call SRT, and identify a single-sequence element essential to replicator function. SRT was detected as early as 2 h after HCMV infection of human fibroblast cells; transcript levels increased by 24 h and continued to increase thereafter. Consistent with its early appearance, treatment of HCMV-infected cells with the viral DNA polymerase inhibitor phosphonoformic acid had no effect on SRT accumulation; however, no SRT was detected in RNA preparations from cycloheximide-treated infected cells. Additional Northern (RNA) analysis localized the 0.2- to 0.25-kb SRT to an apparently noncoding segment near the center of the oriLyt core region. Reverse transcriptase PCR (rapid amplification of cDNA 5' ends [5'-RACE]) identified a single 5' end. In transient-transfection assays, the sequence immediately upstream of SRT functioned as a promoter responsive to HCMV infection when placed upstream of a reporter gene, suggesting that SRT is the product of a discrete transcription unit. RNA ligase-mediated 3'-RACE showed that SRT is not polyadenylated and has heterogeneous 3' ends within a roughly 45-nucleotide window overlapping an oligopyrimidine sequence having counterparts in the lytic-phase replicators of several herpesviruses. Mutation of the oligopyrimidine element showed that it is essential to oriLyt replicator function; it is the only essential single-sequence HCMV oriLyt replicator element described to date. Collectively, the location of SRT near the center of the oriLyt core region, its early expression, its overlapping relationship with a sequence element essential to replicator function, and its similarities to replicator transcripts in other systems suggest the possibility that SRT plays a role in initiating or regulating HCMV lytic-phase DNA synthesis.
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Affiliation(s)
- L Huang
- The David Axelrod Institute, Wadsworth Center for Laboratories and Research, University at Albany School of Public Health, New York 12201-2002, USA
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3
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Reddy R, Singh R, Shimba S. Methylated cap structures in eukaryotic RNAs: structure, synthesis and functions. Pharmacol Ther 1992; 54:249-67. [PMID: 1465477 DOI: 10.1016/0163-7258(92)90002-h] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
There are more than twenty capped small nuclear RNAs characterized in eukaryotic cells. All the capped RNAs appear to be involved in the processing of other nuclear premessenger or preribosomal RNAs. These RNAs contain either trimethylguanosine (TMG) cap structure or methylated gamma phosphate (Mppp) cap structure. The TMG capped RNAs are capped with M7G during transcription by RNA polymerase II and trimethylated further post-transcriptionally. The Mppp-capped RNAs are transcribed by RNA polymerase III and also capped post-transcriptionally. The cap structures improve the stability of the RNAs and in some cases TMG cap is required for transport of the ribonucleoproteins from cytoplasm to the nucleus. Where tested, the cap structures were not essential for their function in processing other RNAs.
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Affiliation(s)
- R Reddy
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030
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4
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Knuth MW, Gunderson SI, Thompson NE, Strasheim LA, Burgess RR. Purification and characterization of proximal sequence element-binding protein 1, a transcription activating protein related to Ku and TREF that binds the proximal sequence element of the human U1 promoter. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)38250-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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5
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Janson L, Pettersson U. Cooperative interactions between transcription factors Sp1 and OTF-1. Proc Natl Acad Sci U S A 1990; 87:4732-6. [PMID: 2191301 PMCID: PMC54191 DOI: 10.1073/pnas.87.12.4732] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We have examined whether the functional synergism between transcription factors Sp1 and OTF-1 involves cooperativity in binding. To demonstrate cooperativity, synthetic enhancers were constructed in which Sp1-binding sites were combined with various OTF-1-binding sites that differed in their binding affinities. The ability of these constructions to activate transcription from the human U2 small nuclear RNA promoter was measured. The results showed that an Sp1-binding site stimulated transcription 2-fold when combined with a high-affinity binding site for OTF-1. When combined with a low-affinity OTF-1-binding site, in contrast, a 20-fold stimulation of transcription was observed. The stimulatory effect of Sp1 was moreover influenced by the distance between the Sp1- and OTF-1-binding sites and the functional cooperation was mirrored by the cooperative formation of OTF-1- and Sp1-specific protein-DNA complexes in vitro. We conclude from these results that the functional cooperation between OTF-1 and Sp1 involves physical interactions between the two transcription factors resulting in cooperative binding. The results thus reveal a mechanism by which Sp1 can modulate transcription.
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Affiliation(s)
- L Janson
- Department of Medical Genetics, Uppsala University, Sweden
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6
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Neuman de Vegvar HE, Dahlberg JE. Initiation and termination of human U1 RNA transcription requires the concerted action of multiple flanking elements. Nucleic Acids Res 1989; 17:9305-18. [PMID: 2587258 PMCID: PMC335133 DOI: 10.1093/nar/17.22.9305] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Sequences in the 5' flanking region of small nuclear RNA (snRNA) genes are responsible for recognition of 3' end signals. Formation of the pre-U1 3' end occurs at the downstream signal closest to the promoter, probably by transcription termination. We have analyzed promoter elements for their participation in formation of the 3' ends of pre-U1 RNA. To do this, a human U1 RNA gene with deletions in individual promoter elements was microinjected into Xenopus laevis oocytes and the resulting RNAs were analyzed by a nuclease S1 protection assay. Each of the promoter elements, except element B (the functional equivalent of a TATA box), was shown to be dispensable for recognition of the snRNA 3' end signal. This latter element was necessary, but not sufficient, for initiation of transcription; so its possible role in termination could not be assessed. Therefore, it is likely that recognition of the 3' end signal is an inherent feature of transcription complexes that initiate at an snRNA promoter.
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7
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Janson L, Weller P, Pettersson U. Nuclear factor I can functionally replace transcription factor Sp1 in a U2 small nuclear RNA gene enhancer. J Mol Biol 1989; 205:387-96. [PMID: 2926813 DOI: 10.1016/0022-2836(89)90349-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Polymerase II transcription of a human gene for the small nuclear RNA U2 is dependent on two different promoter elements: a TATA-equivalent proximal sequence element and a distal enhancer element, which has been shown to contain Sp1- and octamer-binding sites. We have investigated the functional interplay between these transcription factor-binding sites of the enhancer, following transfection of U2 maxigene constructions into HeLa cells. There is a functional non-additive co-operation between the octamer-binding factor and Sp1, which is not dependent on the evolutionally conserved steric arrangement of these binding sites. We demonstrate that the conserved Sp1-binding site of the U2 enhancer can be fully substituted by a nuclear factor I (NFI) binding site, and that the octamer-binding factor functions in stimulating transcription in conjunction with either Sp1 or NFI. Since the octamer-binding factor is most probably the same protein as nuclear factor III (NFIII), the results imply that the NFI/NFIII complex, involved in adenovirus DNA replication, also can function as an efficient activator of transcription.
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Affiliation(s)
- L Janson
- Department of Medical Genetics, Uppsala University, Biomedical Center, Sweden
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8
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Weller P, Bark C, Janson L, Pettersson U. Transcription analysis of a human U4C gene: involvement of transcription factors novel to snRNA gene expression. Genes Dev 1988; 2:1389-99. [PMID: 2850259 DOI: 10.1101/gad.2.11.1389] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have investigated the promoter requirements for in vivo transcription of a human U4C snRNA gene following transfection into HeLa cells. Two elements required for maximal U4C transcription were identified. The first, located upstream of -50, provides a basal level of transcription 2-3% of the full activity, and probably corresponds to the previously identified snRNA gene proximal element. The distal element, centered around -220, acts as a transcriptional enhancer and contains motifs for three previously recognized transcription factors: the octamer-binding protein, NF-A, which binds to motifs in the distal elements of other snRNA genes, and two factors not previously shown to be involved in snRNA gene transcription, cAMP response element binding protein (CREB) and AP-2. The octamer and putative AP-2 motifs are required for maximal transcription of the U4C gene. Specific binding of NF-A and CREB to the motifs in the distal element has been shown in vitro by DNase I and DMS methylation protection footprint competition analyses using HeLa nuclear extracts. The presence of a binding motif for the inducible factor CREB, together with the transcriptional requirement for the putative AP-2 motif, suggests a means by which expression of snRNA genes might be regulated.
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Affiliation(s)
- P Weller
- Department of Medical Genetics, Biomedical Center, Uppsala, Sweden
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9
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Abstract
The transcription of U1 RNA genes was studied in isolated nuclei from mouse myeloma cells. Using a cloned U1b gene as a probe, we showed that isolated nuclei synthesize both U1b and U1a RNA. The U1 RNAs were initiated in vitro, as measured by incorporation of adenosine 5'-O-(2-thiotriphosphate) into U1 RNA. There was transcription of the 3'-flanking region but no transcription of regions directly 5' to the U1 genes. In addition to U1 RNAs of the correct length which were released from the nuclei, there were larger RNAs, presumably resulting from transcription into the 3'-flanking region, which were retained in the nuclei. Chase experiments showed that these longer transcripts were not precursors to mature U1 RNA, a finding consistent with the idea that 3'-end formation is coincident with transcription. During the chase, there was maturation of the 3' ends of U1a and U1b RNAs from slightly longer precursors. In addition to accurate transcription of U1 RNA, there was also synthesis of U2 and U3 RNA. All three of these RNAs were transcribed by RNA polymerase II, as measured by their sensitivity to alpha-amanitin.
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10
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Accurate and efficient 3' processing of U2 small nuclear RNA precursor in a fractionated cytoplasmic extract. Mol Cell Biol 1987. [PMID: 3670307 DOI: 10.1128/mcb.7.9.3131] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The small nuclear RNAs U1, U2, U4, and U5 are cofactors in mRNA splicing and, like the pre-mRNAs with which they interact, are transcribed by RNA polymerase II. Also like mRNAs, mature U1 and U2 RNAs are generated by 3' processing of their primary transcripts. In this study we have investigated the in vitro processing of an SP6-transcribed human U2 RNA precursor, the 3' end of which matches that of authentic human U2 RNA precursor molecules. Although the SP6-U2 RNA precursor was efficiently processed in an ammonium sulfate-fractionated HeLa cytoplasmic S100 extract, the product RNA was unstable. Further purification of the processing activity on glycerol gradients resolved a 7S activity that nonspecifically cleaved all RNAs tested and a 15S activity that efficiently processed the 3' end of pre-U2 RNA. The 15S activity did not process the 3' end of a tRNA precursor molecule. As demonstrated by RNase protection, the processed 3' end of the SP6-U2 RNA maps to the same nucleotides as does mature HeLa U2 RNA.
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11
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Lobo SM, Marzluff WF. Synthesis of U1 RNA in isolated mouse cell nuclei: initiation and 3'-end formation. Mol Cell Biol 1987; 7:4290-6. [PMID: 3437891 PMCID: PMC368111 DOI: 10.1128/mcb.7.12.4290-4296.1987] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The transcription of U1 RNA genes was studied in isolated nuclei from mouse myeloma cells. Using a cloned U1b gene as a probe, we showed that isolated nuclei synthesize both U1b and U1a RNA. The U1 RNAs were initiated in vitro, as measured by incorporation of adenosine 5'-O-(2-thiotriphosphate) into U1 RNA. There was transcription of the 3'-flanking region but no transcription of regions directly 5' to the U1 genes. In addition to U1 RNAs of the correct length which were released from the nuclei, there were larger RNAs, presumably resulting from transcription into the 3'-flanking region, which were retained in the nuclei. Chase experiments showed that these longer transcripts were not precursors to mature U1 RNA, a finding consistent with the idea that 3'-end formation is coincident with transcription. During the chase, there was maturation of the 3' ends of U1a and U1b RNAs from slightly longer precursors. In addition to accurate transcription of U1 RNA, there was also synthesis of U2 and U3 RNA. All three of these RNAs were transcribed by RNA polymerase II, as measured by their sensitivity to alpha-amanitin.
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Affiliation(s)
- S M Lobo
- Department of Chemistry, Florida State University, Tallahassee 32306
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12
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Kleinschmidt AM, Pederson T. Accurate and efficient 3' processing of U2 small nuclear RNA precursor in a fractionated cytoplasmic extract. Mol Cell Biol 1987; 7:3131-7. [PMID: 3670307 PMCID: PMC367947 DOI: 10.1128/mcb.7.9.3131-3137.1987] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The small nuclear RNAs U1, U2, U4, and U5 are cofactors in mRNA splicing and, like the pre-mRNAs with which they interact, are transcribed by RNA polymerase II. Also like mRNAs, mature U1 and U2 RNAs are generated by 3' processing of their primary transcripts. In this study we have investigated the in vitro processing of an SP6-transcribed human U2 RNA precursor, the 3' end of which matches that of authentic human U2 RNA precursor molecules. Although the SP6-U2 RNA precursor was efficiently processed in an ammonium sulfate-fractionated HeLa cytoplasmic S100 extract, the product RNA was unstable. Further purification of the processing activity on glycerol gradients resolved a 7S activity that nonspecifically cleaved all RNAs tested and a 15S activity that efficiently processed the 3' end of pre-U2 RNA. The 15S activity did not process the 3' end of a tRNA precursor molecule. As demonstrated by RNase protection, the processed 3' end of the SP6-U2 RNA maps to the same nucleotides as does mature HeLa U2 RNA.
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Affiliation(s)
- A M Kleinschmidt
- Cell Biology Group, Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts 01545
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13
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The highly conserved U small nuclear RNA 3'-end formation signal is quite tolerant to mutation. Mol Cell Biol 1987. [PMID: 3037343 DOI: 10.1128/mcb.7.6.2070] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Formation of the 3' end of U1 and U2 small nuclear RNA (snRNA) precursors is directed by a conserved sequence called the 3' box located 9 to 28 nucleotides downstream of all metazoan U1 to U4 snRNA genes sequenced so far. Deletion of part or all of the 3' box from human U1 and U2 genes drastically reduces 3'-end formation. To define the essential nucleotides within this box that direct 3'-end formation, we constructed a set of point mutations in the conserved residues of the human U1 3' box. The ability of the various mutations to direct 3'-end formation was tested by microinjection into Xenopus oocytes and transfection into HeLa cells. We found that the point mutations had diverse effects on 3'-end formation, ranging from no effect at all to severe inhibition; however, no single or double point mutation we tested completely eliminated 3'-end formation. We also showed that a rat U3 3' flank can effectively substitute for the human U1 3' flank, indicating that the 3' boxes of the different U snRNA genes are functionally equivalent.
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14
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Ach RA, Weiner AM. The highly conserved U small nuclear RNA 3'-end formation signal is quite tolerant to mutation. Mol Cell Biol 1987; 7:2070-9. [PMID: 3037343 PMCID: PMC365327 DOI: 10.1128/mcb.7.6.2070-2079.1987] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Formation of the 3' end of U1 and U2 small nuclear RNA (snRNA) precursors is directed by a conserved sequence called the 3' box located 9 to 28 nucleotides downstream of all metazoan U1 to U4 snRNA genes sequenced so far. Deletion of part or all of the 3' box from human U1 and U2 genes drastically reduces 3'-end formation. To define the essential nucleotides within this box that direct 3'-end formation, we constructed a set of point mutations in the conserved residues of the human U1 3' box. The ability of the various mutations to direct 3'-end formation was tested by microinjection into Xenopus oocytes and transfection into HeLa cells. We found that the point mutations had diverse effects on 3'-end formation, ranging from no effect at all to severe inhibition; however, no single or double point mutation we tested completely eliminated 3'-end formation. We also showed that a rat U3 3' flank can effectively substitute for the human U1 3' flank, indicating that the 3' boxes of the different U snRNA genes are functionally equivalent.
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15
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Abstract
U1 and U2 snRNAs are thought to be transcribed by RNA polymerase II. A conserved sequence known as the 3' box is located just downstream from the snRNA coding region and directs formation of the 3' end of pre-U1 and pre-U2 snRNA. We show here that a U1 or U2 promoter containing an intact snRNA enhancer is required for the U1 3' box to function efficiently. Promoters for genes encoding mRNAs cannot substitute for the snRNA promoter. Thus snRNAs must be transcribed by a specialized transcription complex that differs from transcription complexes synthesizing mRNAs. Moreover, in contrast to polyadenylated and nonpolyadenylated mRNAs, the 3' ends of pre-snRNAs must be generated either by termination of transcription, or by an RNA processing event intimately coupled to transcription.
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16
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Hernandez N. Formation of the 3' end of U1 snRNA is directed by a conserved sequence located downstream of the coding region. EMBO J 1985; 4:1827-37. [PMID: 2411548 DOI: 10.1002/j.1460-2075.1985.tb03857.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
U1 is a small non-polyadenylated nuclear RNA that is transcribed by RNA polymerase II and is known to play a role in mRNA splicing. The mature 3' end of U1 snRNA is formed in at least two steps. The first step generates precursors of U1 RNA with a few extra nucleotides at the 3' end; in the second step, these precursors are shortened to mature U1 RNA. Here, I have determined the sequences required for the first step. Human U1 genes with various deletions and substitutions near the 3' end of the coding region were constructed and introduced into HeLa cells by DNA transfection. The structure of the RNA synthesized during transient expression of the exogenous U1 gene was analyzed by S1 mapping. The results show that a 13 nucleotide sequence located downstream from the U1 coding region and conserved among U1, U2 and U3 genes of different species is the only sequence required to direct the first step in the formation of the 3' end of U1 snRNA.
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17
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Pedersen N, Hellung-Larsen P, Engberg J. Small nuclear RNAs in the ciliate Tetrahymena. Nucleic Acids Res 1985; 13:4203-24. [PMID: 2409533 PMCID: PMC341306 DOI: 10.1093/nar/13.11.4203] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have isolated and partially characterized a family of small nuclear RNAs (snRNAs) from three different species of the protozoan Tetrahymena. We find six distinct snRNAs ranging in size from 100 to 250 nucleotides. The two largest snRNAs, as well as an abundant, heterogenous group of smaller snRNAs are found in the nucleolar RNA fraction. None of the snRNAs are transcription products of the ribosomal RNA gene or its flanking regions, as shown by hybridization tests. The snRNAs are metabolically stable as determined by pulse/chase experiments and several of them contain a number of modified nuclotides. The snRNAs from Tetrahymena all have slightly different sizes from mammalian snRNAs. The cap structure of the snRNAs from Tetrahymena differs from that of the snRNAs from mammalian cells, but has not yet been fully characterized. The relative amount of snRNAs to total RNA is less in Tetrahymena (greater than 0.1%) than in mammalian cells (2%).
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18
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Kramerov DA, Tillib SV, Lekakh IV, Ryskov AP, Georgiev GP. Biosynthesis and cytoplasmic distribution of small poly(A)-containing B2 RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 824:85-98. [PMID: 2578817 DOI: 10.1016/0167-4781(85)90084-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Previously, we described a small polyadenylated RNA predominantly located in cytoplasm and hybridizing with the ubiquitous B2 sequence of the mouse genome (Kramerov, D.A., Lekakh, I.V., Samarina, O.P. and Ryskov, A.P. (1982) Nucleic Acids Res. 10, 7477-7491). This 180-300 nucleotide long RNA was designated B2 RNA. Here, we demonstrate that B2 RNA is complementary to just one of the strands of cloned B2 sequence. The synthesis of B2 is rather resistant to ultraviolet irradiation of Ehrlich ascites carcinoma cells. The treatment of the cells with alpha-amanitin at a concentration completely blocking the formation of small nuclear RNAs U1, U2 and U3 does not interfere with the B2 RNA synthesis. These results suggest that B2 RNA formation is directly transcribed with the aid of RNA polymerase III, rather than being formed in the course of the processing of large RNA molecules which are known to contain a lot of B2 sequences. We also surprisingly found that the synthesis of up to 50% of long poly(A) +RNA in Ehrlich carcinoma cells is rather resistant to alpha-amanitin. The possible role of genetic elements including B2 sequences able to promote large RNA-polymerase III transcripts is discussed. B2 RNA in the cytoplasm is incorporated into the ribonucleoprotein particles, both small (12-18 S) and heavy. The latter probably correspond to informosomes. After deproteinization of heavy particles, a major part of B2 RNA still cosediments with mRNA and is split from it only after denaturation. We suggest that the B2 RNA of heavy ribonucleoproteins is associated with mRNA by short complementary stretches. About half of the B2 RNA is recovered in the cytoskeletal fraction. The possible role of B2 RNA in mRNA transport or in translation regulation is discussed.
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19
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20
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Eliceiri GL, Ryerse JS. Detection of intranuclear clusters of Sm antigens with monoclonal anti-Sm antibodies by immunoelectron microscopy. J Cell Physiol 1984; 121:449-51. [PMID: 6208207 DOI: 10.1002/jcp.1041210226] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been shown that small nuclear RNA (snRNA) species U1, U2, U4, U5, and U6 are found in the nucleus in the form of small nuclear ribonucleoprotein particles (snRNPs), and that anti-Sm antibodies react with snRNP polypeptides, which are associated with all five snRNAs. We report here a novel intranuclear complex, denoted "Sm cluster," detected by immunostaining with monoclonal anti-Sm antibodies in HeLa cells.
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21
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Earley JM, Roebuck KA, Stumph WE. Three linked chicken U1 RNA genes have limited flanking DNA sequence homologies that reveal potential regulatory signals. Nucleic Acids Res 1984; 12:7411-21. [PMID: 6208531 PMCID: PMC320171 DOI: 10.1093/nar/12.19.7411] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have isolated and characterized a cluster of three closely linked chicken U1 RNA genes from a lambda genomic library. These genes, which are completely collinear and homologous in sequence to chicken U1 RNA, are spaced about 1.8 kilobase pairs (kb) apart in the chicken genome. However, they are not tandemly repeated in that one of the genes has an inverse transcriptional orientation relative to the other two genes which are adjacent in the cluster. A comparison of sequences flanking the 5' ends of these genes reveals that homology is generally limited to a region around position -200 and to the region from -59 to -1. None of the genes possess a "TATA" box near the -25 position. The chicken sequences were compared to various mammalian snRNA genes and significant homology was observed around positions -200, -55 and -20. These data suggest that U1 RNA genes utilize an unusual RNA polymerase II promoter signal and that potential regulatory sequences are located as far as 200 bp upstream from the mature U1 RNA cap site.
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22
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Abstract
It was demonstrated previously that the synthesis of small nuclear RNA (snRNA) species U1 and U2 in human cells is very sensitive to UV radiation. In the present work, the UV sensitivity of U3, U4, and U5 snRNA synthesis is shown to be also high. The synthesis of U1, U2, U3, U4, and U5 snRNAs progressively decreased during the first 2 h after UV irradiation (this was not observed in polyadenylated RNA) and had not returned to normal rates 6 h after UV exposure. In contrast, the restoration of 5.8S rRNA synthesis began immediately after UV irradiation and was essentially complete 6 h later. A small fraction of U1 and U5 (and possibly U2 and U3) snRNA synthesis remained unaffected by high UV doses, when cell radiolabeling began 10 min after UV irradiation. The present data suggest that a factor other than the level of pyrimidine dimers in DNA (possibly, steps in the post-irradiation DNA repair process) plays an important role in the mechanism of UV-induced inhibition of U1-U5 snRNA synthesis.
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23
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Abstract
It was demonstrated previously that the synthesis of small nuclear RNA (snRNA) species U1 and U2 in human cells is very sensitive to UV radiation. In the present work, the UV sensitivity of U3, U4, and U5 snRNA synthesis is shown to be also high. The synthesis of U1, U2, U3, U4, and U5 snRNAs progressively decreased during the first 2 h after UV irradiation (this was not observed in polyadenylated RNA) and had not returned to normal rates 6 h after UV exposure. In contrast, the restoration of 5.8S rRNA synthesis began immediately after UV irradiation and was essentially complete 6 h later. A small fraction of U1 and U5 (and possibly U2 and U3) snRNA synthesis remained unaffected by high UV doses, when cell radiolabeling began 10 min after UV irradiation. The present data suggest that a factor other than the level of pyrimidine dimers in DNA (possibly, steps in the post-irradiation DNA repair process) plays an important role in the mechanism of UV-induced inhibition of U1-U5 snRNA synthesis.
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24
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Abstract
Sequence homology was found by computer analysis between potato spindle tuber viroid (PSTV) RNA and U3B snRNA of Novikoff hepatoma cells. This homology is colinear in arrangement, extends in length to 81% of the entire U3B snRNA molecule and is involved in the PSTV molecule unique sites which, if depicted in terms of the secondary structure of the circular PSTV molecule, reveal a conspicuous regularity in their location. A strong relation in primary structure between PSTV and U3B snRNA is demonstrated by statistical analysis.
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Chandrasekharappa SC, Smith JH, Eliceiri GL. Biosynthesis of small nuclear RNAs in human cells. J Cell Physiol 1983; 117:169-74. [PMID: 6195166 DOI: 10.1002/jcp.1041170206] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We have examined some aspects of the biosynthesis of human small nuclear RNAs (snRNAs). The sensitivity of U5 and U4 snRNA synthesis to alpha-amanitin in whole cells suggests that RNA polymerase II is involved in the synthesis of these RNA species, in addition to that of U1, U2, and U3 snRNA. Two RNA bands were detected, whose properties are compatible with being U3 and U4 RNA precursors. The cytoplasmic U1 RNA precursor (pU1) was retained by an anti-RNP antibody column, while the cytoplasmic precursors to U1 and U2 (pU2) RNA were immunoprecipitated by monoclonal anti-Sm antibodies. Therefore, soon after their transcription, these cytoplasmic RNA precursors assemble with the polypeptides which bear the RNP (pU1) and Sm (pU1 and pU2) antigenic determinants. It has been shown before that, shortly after protein synthesis is interrupted, the apparent cytoplasmic leads to nuclear transition of newly made U2 RNA is inhibited, while U2 RNA transcription is not. The present data indicate that the trimming of the U2 RNA precursor to mature U2 RNA is not affected early after suppression of protein synthesis.
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Reddy R, Busch H. Small nuclear RNAs and RNA processing. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 30:127-62. [PMID: 6198692 DOI: 10.1016/s0079-6603(08)60685-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Abstract
Transcription of U1 small nuclear RNA from a 592 bp fragment of human DNA was analyzed in vivo and in vitro. When injected into Xenopus laevis oocyte nuclei, the cloned DNA is transcribed by RNA polymerase II to make human U1 snRNA. Thus the sequences of this fragment are sufficient for expression of the U1 snRNA gene. Moreover, injection of templates carrying deletions of flanking sequences demonstrates that the DNA sequences required for in vivo transcription are located at least 100 nucleotides upstream from the point corresponding to the 5' end of mature U1 snRNA. In vitro transcription in a HeLa cell extract leads to synthesis not of mature U1 snRNA, but of a larger molecule starting 183 nucleotides upstream from the site corresponding to the 5' end of mature U1 snRNA. Transcription from this upstream promoter also is catalyzed by RNA polymerase II, and is comparable in efficiency with the very strong major late promoter of adenovirus 2. We propose that U1 snRNA is synthesized in vivo as a precursor that is processed by an enzyme or enzymes missing from our extracts.
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Gallinaro H, Lazar E, Jacob M, Krol A, Branlant C. Small RNAs in HnRNP fibrils and their possible function in splicing. Mol Biol Rep 1981; 7:31-9. [PMID: 6166851 DOI: 10.1007/bf00778730] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Several arguments are in favor of a function of snRNA in the processing of premessenger RNA. A large fraction of snRNA is localized in hnRNP which are assumed to be the site of processing. The different snRNA species are not bound to hnRNP in a unique manner but are associated with both proteins and hnRNA which suggests the possibility of metabolic exchanges in the course of processing. There is approximately 1-2 molecules of snRNA per individual hnRNP. We reexamined the possibility that U1A RNA might serve for the alignment of the extremities of the intron sequences of premessenger RNA insuring correct condition for cutting and splicing. We found that only a UCCA (3' leads to 5') sequence at position 8-11 of U1A RNA was complementary to an AG-GU (5' leads to 3') around a putative splice point for 69 different introns sequenced so far. On the basis of secondary structure of U1A RNA, the UCCA sequence would be available for hybridization. The UCCA sequence is also present in U2 RNA and 4.5 S RNAI. It might associate with AG-GU in a manner similar to that of codon-anticodon, the stability of the complex being insured by the configuration of hnRNP. The possible formation of larger hybrids stable by themselves is unlikely upon examination of the nucleotide sequence of various introns adjacent to the splice point. As there is no direct experimental evidence for the function of snRNA in splicing, there considerations are speculative at the present time. The possibility that adenovirus encoded VA RNA would play a role in splicing was also examined. Various arguments suggest that this possibility is rather remote.
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Hellung-Larsen P, Jensen EG, Frederiksen S. Effect of 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole on the synthesis of low molecular weight, RNA components. Biochem Biophys Res Commun 1981; 99:1303-10. [PMID: 6167267 DOI: 10.1016/0006-291x(81)90761-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Bouche G, Caizergues-Ferrer M, Amalric F, Zalta JP, Banville D, Simard R. Synthesis and behaviour of small RNA species of CHO cells submitted to a heat chick. Nucleic Acids Res 1981; 9:1615-25. [PMID: 6164991 PMCID: PMC326786 DOI: 10.1093/nar/9.7.1615] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Incubation of Chinese hamster ovary (CHO) cells for 1 hour at 43 degrees C results in an inhibition of high molecular weight RNA synthesis while most of the ow molecular weight RNAs are still synthesized. In cells returned to 37 degrees C, the transcription of high molecular weight RNA is reinitiated after 7 h recovery. The synthesis of snRNA A, C, D which are transcribed by RNA polymerase B (II) is inhibited in cells incubated at 43 degrees C while the synthesis of 4S, 5S, L and K components is not affected. During the recovery period the synthesis of low molecular weight RNA is increased variously according to the components relative to control cells : x 1.5 for 5S RNA to x 8 for snK. After 9 h recovery at 37 degrees C, snA and SnD are again synthesized but newly synthesized snC does not appear in the nucleus while a putative preC component accumulates in the cytoplasm. On the other hand, the distribution of all the pre-existing low molecular weight RNAs is not affected by the heat shock.
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Hellung-Larsen P, Kulamowicz I, Frederiksen S. Synthesis of low molecular weight RNA components in cells with a temperature-sensitive polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 609:201-4. [PMID: 6157418 DOI: 10.1016/0005-2787(80)90213-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
AF 8 cells are a mutant cell line of baby hamster kidney cells with a temperature-sensitive polymerase II activity. When these cells grow at the non-permissive temperature (40 degrees C) the syntheseis of low molecular weight RNA components D, C and A is preferentially inhibited, whereas the synthesis of rRNA, tRNA, 5 S RNA and component L is affected only a little or not at all. These results indicate that polymerase II catalyzes the synthesis of components D, C and A.
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Gallinaro H, Gattoni R, Stevenin J, Jacob M. Small nuclear RNA and VA RNA in nuclear ribonucleoprotein fibrils from adenovirus-2 infected HeLa cells. Biochem Biophys Res Commun 1980; 95:20-6. [PMID: 6158316 DOI: 10.1016/0006-291x(80)90698-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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