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Berger MR, Alvarado R, Kiss DL. mRNA 5' ends targeted by cytoplasmic recapping cluster at CAGE tags and select transcripts are alternatively spliced. FEBS Lett 2019; 593:670-679. [PMID: 30810230 DOI: 10.1002/1873-3468.13349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/04/2019] [Accepted: 02/22/2019] [Indexed: 11/07/2022]
Abstract
Until cytoplasmic recapping was discovered, decapping was thought to irreversibly destine an mRNA to degradation. Contradicting this idea, we readily observe mRNAs targeted by cytoplasmic capping in uncapped, yet stable forms. 5' rapid amplification of cDNA ends (RACE) shows that nearly all uncapped ends correspond to capped analysis of gene expression tags and that the recapping of ZNF207 mRNA may be restricted to a single splice isoform. Here, a modified RACE approach detected uncapped 5' RNA ends mapping to 46 mRNAs in cells expressing a dominant negative cytoplasmic capping enzyme and in normal cells. Eleven of 46 cloned mRNAs also contained splice isoform-limiting sequences. Collectively, these data reinforce earlier work and suggest that alternative splicing may play a role in targeting transcripts for - and/or determining the position of - cytoplasmic capping.
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Affiliation(s)
- Mikaela R Berger
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Rolando Alvarado
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, TX, USA
| | - Daniel L Kiss
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, TX, USA
- Weill Cornell Medical College, Houston Methodist Research Institute, TX, USA
- Institute of Academic Medicine, Houston Methodist Research Institute, TX, USA
- Houston Methodist Cancer Center, Houston Methodist Research Institute, TX, USA
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2
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The messenger RNA decapping and recapping pathway in Trypanosoma. Proc Natl Acad Sci U S A 2015; 112:6967-72. [PMID: 26038549 DOI: 10.1073/pnas.1424909112] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The 5' terminus of trypanosome mRNA is protected by a hypermethylated cap 4 derived from spliced leader (SL) RNA. Trypanosoma brucei nuclear capping enzyme with cap guanylyltransferase and methyltransferase activities (TbCgm1) modifies the 5'-diphosphate RNA (ppRNA) end to generate an m7G SL RNA cap. Here we show that T. brucei cytoplasmic capping enzyme (TbCe1) is a bifunctional 5'-RNA kinase and guanylyltransferase that transfers a γ-phosphate from ATP to pRNA to form ppRNA, which is then capped by transfer of GMP from GTP to the RNA β-phosphate. A Walker A-box motif in the N-terminal domain is essential for the RNA kinase activity and is targeted preferentially to a SL RNA sequence with a 5'-terminal methylated nucleoside. Silencing of TbCe1 leads to accumulation of uncapped mRNAs, consistent with selective capping of mRNA that has undergone trans-splicing and decapping. We identify T. brucei mRNA decapping enzyme (TbDcp2) that cleaves m7GDP from capped RNA to generate pRNA, a substrate for TbCe1. TbDcp2 can also remove GDP from unmethylated capped RNA but is less active at a mature cap 4 end and thus may function in RNA cap quality surveillance. Our results establish the enzymology and relevant protein catalysts of a cytoplasmic recapping pathway that has broad implications for the functional reactivation of processed mRNA ends.
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3
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Sibbritt T, Patel HR, Preiss T. Mapping and significance of the mRNA methylome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:397-422. [PMID: 23681756 DOI: 10.1002/wrna.1166] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/25/2022]
Abstract
Internal methylation of eukaryotic mRNAs in the form of N6-methyladenosine (m(6)A) and 5-methylcytidine (m(5)C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high-throughput sequencing-based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m(6)A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m(5)C and m(6)A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post-transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA-binding proteins and microRNAs. The methyltransferase (MTase) METTL3 'writes' m(6)A marks on mRNA, whereas the demethylase FTO can 'erase' them. The RNA:m(5)C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics.
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Affiliation(s)
- Tennille Sibbritt
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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4
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Gupta KC, Roy P. Alternate capping mechanisms for transcription of spring viremia of carp virus: evidence for independent mRNA initiation. J Virol 2010; 33:292-303. [PMID: 16789187 PMCID: PMC288546 DOI: 10.1128/jvi.33.1.292-303.1980] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two alternate mechanisms of mRNA capping for spring viremia of carp virus have been observed. Under normal reaction conditions, a ppG residue of the capping GTP is transferred to a pA moiety of the 5' termini of mRNA transcripts. However, in reaction conditions where GppNHp is used instead of GTP, an alternate capping mechanism occurs whereby a pG residue of the capping GTP is transferred to a ppA moiety of the transcripts. The first mechanism is identical to that described previously for vesicular stomatitis virus (G. Abraham, D. P. Rhodes, and A. K. Banerjee, Nature [London] 255:37-40, 1975; A. K. Banerjee, S. A. Moyer, and D. P. Rhodes, Virology 61:547-558, 1974), and thus appears to be a conserved function during the evolution of rhabdoviruses. The alternate mechanism of capping indicates not only that capping can take place by two procedures, but also that the substrate termini have di- or triphosphate 5' ends, indicating that they are probably independently initiated. An analog of ATP, AppNHp, has been found to completely inhibit the initiation of transcription by spring viremia of carp virus, suggesting that a cleavage between the beta and gamma phosphates of ATP is essential for the initiation of transcription. However, in the presence of GppNHp, uncapped (ppAp and pppAp), capped (GpppAp), and capped methylated (m7GpppAmpAp and GpppAmpAp) transcripts are detected. Size analyses of oligodeoxythymidylic acid-cellulose-bound transcripts resolved by formamide gel electrophoresis demonstrated that full-size mRNA transcripts are synthesized as well as larger RNA species. The presence of GppNHp and S-adenosylhomocysteine in reaction mixtures did not have any effect on the type of unmethylated transcription products. Our results favor a transcription model postulated previously (D. H. L. Bishop, in H. Fraenkel-Conrat and R. R. Wagner, ed., Comprehensive Virology, vol. 10, Plenum Press, New York, 1977; D. H. L. Bishop and A. Flamand, in D. C. Burke and W. C. Russell, ed., Control Processes in Virus Multiplication, Cambridge University Press, Cambridge, 1975; D. H. L. Bishop and M. S. Smith, in D. Nayak, ed., The Molecular Biology of Animal Viruses, Marcel Dekker, New York, 1977; P. Roy and D. H. L. Bishop, J. Virol. 11:487-501, 1973) in which mRNA synthesis is initiated independently; they do not support a model for transcripts being synthesized by plus-strand cleavage (A. K. Banerjee, G. Abraham, and R. J. Colonno, J. Gen. Virol. 34:1-8, 1977; A. K. Banerjee, R. J. Colonno, D. Testa, and M. T. Franze-Fernandez, in B. M. J. Mahy and R. D. Barry, ed., Negative Strand Viruses and the Host Cells, Academic Press, London, 1978).
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Affiliation(s)
- K C Gupta
- Departments of Microbiology and Public Health, University of Alabama in Birmingham, Birmingham, Alabama 35294
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5
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Schoenberg DR, Maquat LE. Re-capping the message. Trends Biochem Sci 2009; 34:435-42. [PMID: 19729311 DOI: 10.1016/j.tibs.2009.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 05/13/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
Abstract
The 5'-cap structure that typifies all polymerase II-transcribed RNAs plays important roles in pre-mRNA processing and mRNA export, translation and quality control. Removal of the cap is a regulated process that is considered to be the first irreversible step in mRNA decay. An emerging view challenges this idea: mRNAs have been identified in mammalian cells that lack sequences from their 5' ends but nevertheless appear to be modified with a cap or cap-like structure. Furthermore, a cytoplasmic form of capping enzyme was recently identified that, together with a novel kinase, generates capped ends from cleaved RNAs. These and other findings provide evidence for re-capping and its possible functions.
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Affiliation(s)
- Daniel R Schoenberg
- Department of Molecular and Cellular Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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6
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Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA. Mol Cell Biol 2009; 29:2155-67. [PMID: 19223470 DOI: 10.1128/mcb.01325-08] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endonuclease decay of nonsense-containing beta-globin mRNA in erythroid cells generates 5'-truncated products that were reported previously to have a cap or caplike structure. We confirmed that this 5' modification is indistinguishable from the cap on full-length mRNA, and Western blotting, immunoprecipitation, and active-site labeling identified a population of capping enzymes in the cytoplasm of erythroid and nonerythroid cells. Cytoplasmic capping enzyme sediments in a 140-kDa complex that contains a kinase which, together with capping enzyme, converts 5'-monophosphate RNA into 5'-GpppX RNA. Capping enzyme shows diffuse and punctate staining throughout the cytoplasm, and its staining does not overlap with P bodies or stress granules. Expression of inactive capping enzyme in a form that is restricted to the cytoplasm reduced the ability of cells to recover from oxidative stress, thus supporting a role for capping in the cytoplasm and suggesting that some mRNAs may be stored in an uncapped state.
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7
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Caldwell DC, Emerson CP. The role of cap methylation in the translational activation of stored maternal histone mRNA in sea urchin embryos. Cell 1985; 42:691-700. [PMID: 2411426 DOI: 10.1016/0092-8674(85)90126-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cap methylation was examined in the early sea urchin embryo. Nucleotide analyses of 3H-methyl methionine-labeled RNA in two-cell embryos and in unfertilized eggs show that fertilization activates the cap methylation of about 10(7) RNA molecules. Greater than 37% of methyl-labeled RNAs following fertilization hybridize with so-called early histone genes H1, H4, and H2B, which encode a subpopulation of the maternal mRNA molecules. Activation of RNA cap methylation is inhibited by aphidicolin, but not by actinomycin D, suggesting that this process is temporally coordinated with DNA replication, but independent of RNA transcription. These results indicate that the translational activation of maternal early histone mRNA during fertilization is a consequence of cap methylation of mRNAs incompletely formed during oogenesis.
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8
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Ilyin YV, Georgiev GP. The main types of organization of genetic material in eukaryotes. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1982; 12:237-87. [PMID: 6282534 DOI: 10.3109/10409238209108708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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9
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Wallace JC, Wood WM, Edmonds M. 5'-Terminal cap structures of oligo(uridylic acid)-containing messenger ribonucleic acid from HeLa cells: comparison with other ribonucleic acid subpopulations. Biochemistry 1981; 20:5364-8. [PMID: 6170325 DOI: 10.1021/bi00522a002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The 5'-terminal cap structures of 32P-labeled oligo(uridylic acid)-containing messenger ribonucleic acid [oligo(U+)mRNA] isolated from HeLa cell polyadenylated [poly(A+)] mRNA were analyzed and compared to those of the poly(A+) mRNA. A method employing P1 nuclease, alkaline phosphatase, and adsorption to activated charcoal showed that the types of cap core (m7 GpppXm) in oligo(U+) mRNA were essentially identical with those in poly(A+) mRNA. Analysis of RNase T2 digestion products of oligo(U+) mRNA demonstrated the presence of both cap 1 (m7GpppXmpYp) and cap 2 (m7GpppXmpYmpZp) in this subpopulation, confirming its cytoplasmic location. The base compositions of these two types of caps were different from each other and nonrandom but did not differ significantly between oligo(U+) and poly(A+) m RNA. The only observed difference between the mRNA populations was a higher ratio of cap 1 and cap 2 in the former. Possible implications of these findings for the relationship between oligo(U+) mRNA and poly(A+) mRNA are discussed.
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10
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Gupta KC, Roy P. Synthesis of capped and uncapped methylated oligonucleotides by the virion transcriptase of spring viremia of carp virus, a rhabdovirus. Proc Natl Acad Sci U S A 1981; 78:4758-62. [PMID: 6946423 PMCID: PMC320242 DOI: 10.1073/pnas.78.8.4758] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Capped and uncapped methylated oligonucleotides, five and six nucleotides in length, were synthesized in vitro in spring viremia of carp virus transcription reaction mixtures containing ATP + CTP, ATP + CTP + GTP, or ATP + CTP + UTP, but not in any other combinations of two or three ribonucleoside triphosphates. The oligonucleotides that have been characterized are consistent with the structures: m7GpppAmpNpCpNpN, GpppAmpNpCpNpN, pppAmpNpCpNpN, and ppAmpNpCpNpN--i.e., similar to those of the termini of transcripts made in complete reaction mixtures. Because both capped and uncapped methylated oligonucleotides were synthesized, it can be concluded that methylation of the penultimate nucleotide can precede capping and methylation of the capping nucleotide. Our results also indicate that capping and methylation are processes that can take place prior to mRNA chain completion.
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11
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Contreras R, Fiers W. Initiation of transcription by RNA polymerase II in permeable, SV40-infected or noninfected, CVI cells; evidence for multiple promoters of SV40 late transcription. Nucleic Acids Res 1981; 9:215-36. [PMID: 6259623 PMCID: PMC326688 DOI: 10.1093/nar/9.2.215] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
CV1 cells were made permeable by treatment with lysolecithin and incubated in a transcription mixture containing ribonucleoside triphosphates including ATP or GTP 32P-labeled either in the alpha or beta position. 5'-terminal cap structures (7mGpgamma pbeta palpha X) on newly synthesized RNA were analyzed by digestion with nuclease P1 or with ribonuclease T2/bacterial alkaline phosphatase. Cap structures obtained after labeling with alpha-32P-GTP show that the 32P is found only adjacent to the 7mG residue (i.e., in the gamma position) and adjacent to the penultimate Gm or G nucleotide (i.e., in the alpha position). Analysis of RNA synthesized in the presence of beta-32P-ATP, however, shows GpppA cap structures which are labeled only in the beta position. In the presence of beta-32-p-GTP, only GpppG structures are labeled; these findings exclude the hypothesis that caps are synthesized from GTP and a monophosphate 5'-terminal RNA molecule. The results imply that the initial transcripts are used for cap formation, which indicates that the large majority (if not all) of capping sites correspond to initiation sites for transcription. In cells infected with wild-types SV40 the distribution of virus-specific caps is similar when labeled either with beta-32P-ATP or with alpha-32P-GTP or with 32p-phosphate. Thus, evidence is presented that heterogeneity of the cap structures in late SV40 is a consequence of independent initiation events and not of processing of a primary transcript followed by capping of the 5' ends generated.
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12
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13
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Venkatesan S, Moss B. Donor and acceptor specificities of HeLa cell mRNA guanylyltransferase. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)85815-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Haugland RA, Cline MG. Post-transcriptional modifications of oat coleoptile ribonucleic acids. 5'-Terminal capping and methylation of internal nucleosides in poly(A)-rich RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 104:271-7. [PMID: 6154573 DOI: 10.1111/j.1432-1033.1980.tb04425.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Evidence is presented for the occurrence of 5'-terminal capping structures in poly(A)-rich RNAs from oat coleoptile tissue. Similar to the cap structures in mRNA from other eukaryotic organisms, the 5' terminus of these oat coleoptile RNA molecules consists of 7-methylguanosine joined 5' to 5' with the adjacent (penultimate) nucleoside by means of three phosphate groups in two pyrophosphate linkages. The penultimate nucleoside contains primarily purine bases, but small amounts of pyrimidines (cytidine) are also detectable. Some monophosphorylated 5'-termini were also detected, however, they appear to occur as a result of RNA degradation. In addition to the 5 cap, oat RNA molecules are also post-transcriptionally modified with a low frequency of N6-methylations of internal adenosines.
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15
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Flavell AJ, Cowie A, Arrand JR, Kamen R. Localization of three major cappe 5' ends of polyoma virus late mRNA's within a single tetranucleotide sequence in the viral genome. J Virol 1980; 33:902-8. [PMID: 6251254 PMCID: PMC288615 DOI: 10.1128/jvi.33.2.902-908.1980] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequences at the 5' ends of polyoma virus late mRNA's were determined by direct RNA sequencing of decapped and 5'-(32)P-labeled RNase T1 oligoribonucleotides. Virus-specific polyadenylated cytoplasmic RNA, which was isolated from mouse cells late during productive infection, was enzymatically or chemically treated to specifically remove the cap structure (m(7)Gppp). The unblocked 5' ends of the viral mRNA's were then labeled enzymatically with (32)P, and the RNAs were digested with RNase T1 and fingerprinted. Three oligonucleotides derived from capped termini were isolated, and their sequences were determined to be pGmACAUUUUCUAUUUUAAGp, p(m)AmCAUUUUCUAUUUUAAGp, and p(m)AmUUUUCUAUUUUAAGp. These oligonucleotides comprise a staggered set with members 15, 17, and 18 nucleotides long, which share a common 3' sequence for 15 nucleotides. The sequences correspond exactly to the polyoma virus DNA sequence (Arrand et al., J. Virol. 33:606-618, 1980) from 66.79 to 66.46 map units (between 75 and 92 nucleotides preceding the ATG initiation codon for the capsid protein VP2). Previous results showed that the sequence between 13 and 64 nucleotides preceding the VP2 initiation codon corresponds to oligonucleotides reiterated in the leader sequence which is spliced onto the bodies of the three functionally distinct viral late mRNA's (Flavell et al., Cell 16:357-372, 1979; Legon et al., Cell 16:373-388, 1979). The three capped oligonucleotides we sequenced are derived from the first large predicted T1 oligonucleotide 5' to those detected in the leader sequence. The occurrence of a cap at each purine of a single tetranucleotide sequence reflects micro-heterogeneity either in transcriptional initiation or in processing cleavage involved in cap syntheses.
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16
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Shuman S, Hurwitz J. 5'-Hydroxyl polyribonucleotide kinase from HeLa cell nuclei. Purification and properties. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86721-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Surrey S, Ginzburg I, Nemer M. Ribosomal RNA synthesis in pre- and post-gastrula-stage sea urchin embryos. Dev Biol 1979; 71:83-99. [PMID: 467793 DOI: 10.1016/0012-1606(79)90084-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Scherrer K, Imaizumi-Scherrer MT, Reynaud CA, Therwath A. On pre-messenger RNA and transcriptions. A review. Mol Biol Rep 1979; 5:5-28. [PMID: 379595 DOI: 10.1007/bf00777484] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
From the present review integrating old and new data emerge a few principles of gene expression in eukaryotes, and an infinite variety of possible mechanistic details generating the overal pattern. The few principles, most of which are not fundamentally new, may thus be summarized. 1) The eukaryotic genome is subdivided into transcriptional units: into transcriptons which are subject to individual activation controlled at DNA level. 2) Viral genomes may contain one or a few transcriptons, while cells of multicellular organisms contain from 3 x 10(3) in diptera up to an estimated 2 x 10(5) in birds and mammals. 3) Transcriptons may include one or several coding sequences. 4) Transcriptons vary considerably in size: in mammals and birds their size spectrum falls into the 2,000 to 20,000 bp range. 5) Units of coding information constituting one message (genes) and, possibly, units of regulative information are frequently broken up and stored within the transcripton in sub-genic blocks (of so far unknown significance) in general located at a certain distance from the 5' and 3' transcript terminals which are determined by the promotor and terminator signals. 6) The gene, in its specific definition as the functional unit underlying the phenotype, is in general constituted posttranscriptionally by the processing mechanisms from the mosaic of its genomic subunits in the transcripton; segments of coding, service and regulative sequences are recombined within themselves and with each other, polygenic transcripts separate into their unit messages. 7) Activated transcriptons produce pre-mRNA; these primary transcripts are colinear with the DNA of the transcriptional unit. 8) Primary pre-mRNA is processed into secondary pre-mRNA's by extragenic cleavage and intragenic ("splicing") processing, giving rise stepwise to functional mRNA. During this process chemical modifications as methylation, 5'-terminal capping and 3'-terminal polyadenylation take place. 9) Translation yields either potentially functional polypeptides or polycistronic polyproteins subject to further processing. 10) Processing is a regulated process; it involves many of the possible phases and mechanisms of post-transcriptional regulation (cf. 39, 40).
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19
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Lev Z, Kamen R, Manor H. Topography of polyoma virus-specific giant nuclear RNA molecules containing poly(A) sequences. Virology 1979; 93:445-57. [PMID: 222050 DOI: 10.1016/0042-6822(79)90248-4] [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: 12/13/2022]
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20
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Nikolaev N, Georgiev OI, Venkov PV, Hadjiolov AA. The 37 S precursor to ribosomal RNA is the primary transcript of ribosomal RNA genes in Saccharomyces cerevisiae. J Mol Biol 1979; 127:297-308. [PMID: 372542 DOI: 10.1016/0022-2836(79)90331-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Lebowitz P, Weissman SM. Organization and transcription of the simian virus 40 genome. Curr Top Microbiol Immunol 1979; 87:43-172. [PMID: 232871 DOI: 10.1007/978-3-642-67344-3_3] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
MESH Headings
- Antigens, Viral/genetics
- Base Sequence
- Cell Transformation, Neoplastic
- Cell Transformation, Viral
- DNA, Circular/analysis
- DNA, Circular/genetics
- DNA, Viral/analysis
- DNA, Viral/genetics
- Genes, Viral
- Genetic Code
- Hybridization, Genetic
- Nucleotides/analysis
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Viral/analysis
- RNA, Viral/genetics
- Simian virus 40/analysis
- Simian virus 40/genetics
- Templates, Genetic
- Transcription, Genetic
- Viral Proteins/analysis
- Viral Proteins/genetics
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22
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Ghosh PK, Reddy VB, Swinscoe J, Lebowitz P, Weissman SM. Heterogeneity and 5'-terminal structures of the late RNAs of simian virus 40. J Mol Biol 1978; 126:813-46. [PMID: 218021 DOI: 10.1016/0022-2836(78)90022-0] [Citation(s) in RCA: 347] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Giorno R, Ott G, Sauerbier W. Size analysis of heterogeneous nuclear RNA in an aqueous gel system. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 521:235-40. [PMID: 718928 DOI: 10.1016/0005-2787(78)90266-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have analyzed the size distribution of heterogeneous nuclear RNA (hnRNA) from cultured murine cells in an aqueous gel system consisting of 1.8% polyacrylamide and 0.5% agarose. hnRNA, labeled in vivo with 32P at a low specific activity, was labeled in vitro at its 3'-end with NaB3H4, and fractionated by gel electrophoresis. The ratio of log 32P/3H cpm was determined for each gel fraction and shown to be linearly related to distance migrated. The ratio of 32P/3H cpm was used to predict the molecular weight of 28-S and 18-S RNAs and shown to be within approx. 10% of the known molecular weight. Denaturation of hnRNA with heat or dimethyl sulfoxide gave similar number and weight average molecular weight when analyzed by gel electrophoresis. The same hnRNA analyzed by sucrose gradient velocity sedimentation had a similar number average molecular weight but much higher weight average molecular weight.
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24
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Molnár J, Bajszár G, Marczinovits I, Szabó G. Cleavage of pre-mRNA sequences by ribonucleases bound to nuclear RNP particles of rat liver. Mol Biol Rep 1978; 4:157-61. [PMID: 739982 DOI: 10.1007/bf00777517] [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: 12/24/2022]
Abstract
The 30S nuclear RNP particles from rat liver have been shown to split the double-stranded- (ds) and single-stranded (ss) sequences of nuclear pre-mRNA. Experiments performed in vitro have demonstrated that 1) a 5'-exonuclease and an endonuclease specific for double-stranded pre-mRNA sequences exist in the 30S pre-mRNP particles; 2) in dsRNA monophosphorylated 5'-termini arose in the course of incubation with 30S RNP and most of the products remained double-stranded. The analysis of terminal pNp nucleotides revealed a relatively high ratio of pPyp in the cleaved dsRNA, whereas the nucleosides in 5'-terminal pNp of ssRNA showed nearly random distribution. Our results provide a possible explanation for the appearance of pNp termini during the processing of nuclear pre-mRNA of mammalian cells.
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Dreyer C, Hausen P. Inhibition of mammalian RNA polymerase by 5,6-dichlororibofuranosylbenzimidazole (DRB) and DRB triphosphate. Nucleic Acids Res 1978; 5:3325-35. [PMID: 704359 PMCID: PMC342252 DOI: 10.1093/nar/5.9.3325] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
DRB triphosphate inhibits activity of isolated RNA polymerase B, and, to a lesser extent, that of polymerase A. The same holds true for transcription in isolated nuclei. It does not act as an initiation inhibitor. In all cases, high concentrations of DRB triphosphate are required. Cells do not phosphorylate DRB to a measurable extent. hn RNA resistant to DRB is initiated with both ATP and GTP in the presence of the drug. These experiments render the hypothesis unlikely that DRB triphosphate in the cell specifically interferes with the initiation reaction of polymerase B.
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26
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Bachellerie JP, Amalric F, Caboche M. Biosynthesis and utilization of extensively undermethylated poly(A)+ RNA in CHO cells during a cycloleucine treatment. Nucleic Acids Res 1978; 5:2927-43. [PMID: 693324 PMCID: PMC342216 DOI: 10.1093/nar/5.8.2927] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The role of RNA methylations in the control of mRNA maturation and incorporation into polysomes has been investigated through a study of the effects in vivo of cycloleucine, a specific inhibitor of S-adenosyl-methionine mediated methylation. During the cycloleucine treatment, the rate of biosynthesis of hnRNA and its subsequent polyadenylation were only slightly reduced as compared with untreated cells. However a significant lag-time in the cytoplasmic appearance of poly(A)+ undermethylated molecules was observed, in parallel with a transient shift in the average size of hnRNA towards higher molecular weight. Nevertheless, the total amount of pulse-labelled poly(A)+ mRNA transferred to cytoplasm after a long chase time (3 h.) was approximately the same for both cycloleucine-treated and control cells. Extensively undermethylated poly(A)+ cytoplasmic RNAs, possessing a 5' terminal cap were incorporated into polysomes in proportions very similar to control messenger molecules. These results suggest that a normal level of methylation is not stringently required for the production of the functional mRNA molecules although it appears to be of importance for the kinetics of the maturational process.
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27
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HeLa cell RNA (2‘-O-methyladenosine-N6-)-methyltransferase specific for the capped 5‘-end of messenger RNA. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34652-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Monroy G, Spencer E, Hurwitz J. Purification of mRNA guanylyltransferase from vaccinia virions. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34745-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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29
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Dreyer C, Hausen P. On the activity of RNA polymerase B in lysates from Ehrlich ascites cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 86:241-53. [PMID: 658042 DOI: 10.1111/j.1432-1033.1978.tb12305.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Transcription by endogenous RNA polymerase B in lysates of Ehrlich ascites cells was investigated. The enzyme exhibits two salt optima at 0.025 M and at 0.3 M (NH4)2SO4 respectively. Preincubation of the cells with the nucleoside analogue 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole results in an inactivation of the polymerase molecules active under condition of low salt. This indicates two functional states of the enzyme in vivo. Initiations of RNA chains by polymerase B do not occur in vitro as judged by the incorporation of [beta-32P]GTP. Thus the two functional states seem to be both elongating polymerase molecules. Polymerase B does not occur in the lysates in a state ready to initiate on an exogenous template, in contrast to polymerase A and C which do occur in free form. Pretreatment with dichlororibofuranosylbenzimidazole in vivo does not result in an accumulation of free polymerase B.
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30
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Levis R, Penman S. 5'-terminal structures of poly(A)+ cytoplasmic messenger RNA and of poly(A)+ and poly(A)- heterogeneous nuclear RNA of cells of the dipteran Drosophila melanogaster. J Mol Biol 1978; 120:487-515. [PMID: 418182 DOI: 10.1016/0022-2836(78)90350-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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31
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32
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Heinrich PC, Gross V, Northemann W, Scheurlen M. Structure and function of nuclear ribonucleoprotein complexes. Rev Physiol Biochem Pharmacol 1978; 81:101-34. [PMID: 347552 DOI: 10.1007/bfb0034092] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Kaehler M, Coward J, Rottman F. In vivo inhibition of Novikoff cytoplasmic messenger RNA methylation by S-tubercidinylhomocysteine. Biochemistry 1977; 16:5770-5. [PMID: 201277 DOI: 10.1021/bi00645a019] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The analogue S-tubercidinylhomocysteine (STH) has been used to study the methylation of mRNA in vivo. Partial inhibition of cytoplasmic poly(A)-RNA methylation was observed using a level of inhibitor which still permitted cell growth. Characterization of the partially methylated mRNA indicated the presence of cap structures lacking 2'-O-methylnucleosides, m7GpppN', which are normally not found in mammalian mRNA. Inhibition of additional methylated sites in mRNA at the second 2'-O-methynucleoside, and at internal N6-methyladenosine was also observed Methylation of 7-methylguanosine was not affected under the conditions used in these experiments. The methylnucleoside composition of cap structures differed in STH-inhibited and uninhibited cells. These results indicate that a completely methylated cap is not required for transport of mRNA into the cytoplasm. Furthermore, it may now be possible to assess in vivo the sequential nature of mRNA methylation and its potential role in mRNA processing.
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34
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Nienhuis AW, Benz EJ. Regulation of hemoglobin synthesis during the development of the red cell (first of three parts). N Engl J Med 1977; 297:1318-28. [PMID: 335250 DOI: 10.1056/nejm197712152972404] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Amalric F, Bachellerie JP, Caboche M. RNA methylation and control of eukaryotic RNA biosynthesis: processing and utilization of undermethylated tRNAs in CHO cells. Nucleic Acids Res 1977; 4:4357-70. [PMID: 600798 PMCID: PMC343246 DOI: 10.1093/nar/4.12.4357] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The role of RNA methylations in the control of tRNA production and utilization for protein biosynthesis has been investigated through a study of the effects in vivo of cycloleucine a specific and potent inhibitor of S adenosyl-methionine mediated methylation. During the cycloleucine treatment, the rate of appearance of newly synthetized tRNAs into the cytoplasm is markedly reduced (about 50%). These molecules are extensively (more than 90%) undermethylated and are integrated into polysomes, but at a slower rate than normally methylated tRNAs.
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36
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Studies of low molecular weight RNA from cells infected with adenovirus 2. II. Heterogeneity at the 5' end of VA-RNA I. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)38342-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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37
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Schibler U, Perry RP. The 5'-termini of heterogeneous nuclear RNA: a comparison among molecules of different sizes and ages. Nucleic Acids Res 1977; 4:4133-49. [PMID: 600792 PMCID: PMC343230 DOI: 10.1093/nar/4.12.4133] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The composition of the 5' polyphosphorylated and capped termini of pulse labeled hnRNA from mouse L cells was analyzed by two-dimensional electrophoresis. Purine tri- and diphosphates: pppG, pppA, ppG and ppA; as well as four varieties of cap structure: m7GpppXm, Xm = Gm, (m6) Am, Cm and Um, were detected. With increasing labeling time the relative proportion of hnRNA molecules with tri- and diphosphorylated 5' ends decreases and the relative proportion of capped hnRNA increases, indicating that caps are metabolically more stable than the polyphosphate termini. About half of the hnRNA molecules that are labeled within 2 hr have capped ends. This finding, together with results of earlier kinetic and structural studies, implies that a relatively high proportion of the labeled hnRNA molecules are mRNA precursors. Large hnRNA molecules exhibit a higher proportion of capped ends and a lower proportion of 5'-triphosphate ends as compared to small hnRNA. Given the lower stability of triphosphate termini relative to caps, this result may mean that capping of some hnRNA molecules can occur before the completion of transcription.
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38
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Schibler U, Kelley DE, Perry RP. Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cells. J Mol Biol 1977; 115:695-714. [PMID: 592376 DOI: 10.1016/0022-2836(77)90110-3] [Citation(s) in RCA: 202] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Kerr IM, Brown RE, Hovanessian AG. Nature of inhibitor of cell-free protein synthesis formed in response to interferon and double-stranded RNA. Nature 1977; 268:540-2. [PMID: 196217 DOI: 10.1038/268540a0] [Citation(s) in RCA: 169] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Pettersson RF, Flanegan JB, Rose JK, Baltimore D. 5'-Terminal nucleotide sequences of polio virus polyribosomal RNA and virion RNA are identical. Nature 1977; 268:270-2. [PMID: 196211 DOI: 10.1038/268270a0] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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Furuichi Y, Shatkin AJ. 5'-termini of reovirus mRNA: ability of viral cores to form caps post-transcriptionally. Virology 1977; 77:566-78. [PMID: 855185 DOI: 10.1016/0042-6822(77)90482-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Perry RP, Bard E, Hames BD, Kelly DE, Schibler U. The relationship between hnRNA and mRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:275-92. [PMID: 1019347 DOI: 10.1016/s0079-6603(08)60925-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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43
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Chan L, Harris SE, Rosen JM, Means AR, O'Malley BW. Processing of nuclear heterogeneous RNA: recent developments. Life Sci 1977; 20:1-15. [PMID: 319316 DOI: 10.1016/0024-3205(77)90123-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Zuckerkandl E. Gene control in eukaryotes and the c-value paradox "excess" DNA as an impediment to transcription of coding sequences. J Mol Evol 1976; 9:73-104. [PMID: 798041 DOI: 10.1007/bf01796124] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ways in which control of gene activity may lead to the observed high DNA content per haploid eukaryote genome are examined. It is proposed that deoxyribonucleoprotein (DNP) acts as a barrier to transcription at two distinct structural levels. At the lower level, melting of the nucleosome supercoil (quaternary structure) and of the nucleosomes (tertiary structure) might be brought about by the process of transcription itself. After unwinding the barrier section, the polymerase would eventually reach the structural gene. The transcripts of noncoding sequences, at least as far as their "unique" sequence components are concerned, may thus have filled their main function through the very process of transcription. The possibility of an inverse relationship between the length of the DNP barrier and the rates of transcription of the coding sequences is to some extent supported by available data. Different modes of coordination between the transcription of mRNA and of hnRNA from a single functional unit of gene action (funga) are considered. An analysis of gene control at high structural levels of DNP is made on the basis of other data, in relation to the concepts of eurygenic and stenogenic control. The concept of a euryon is introduced, namely of a set of linked fugas under common eurygenic control. Structure of order higher than quaternary can be inferred to exist in larger chromomeres of polytene chromosomes and in corresponding sections of ordinary chromosomes. Only moderate amounts of highest order interphase euchromatic structure are likely to be able to be accomodated in average chromomeres and none in very thin chromomeres. Puffs are interpreted as the melting of highest order interphase structure, and the absence of puffs during transcription as the absence of this highest order structure in the resting state of the chromomeres. Genes that are constantly active in all tissues may dispense with highest order interphase structure and with the corresponding control mechanism, and the fugas involved thus may not puff. Puffs, large chromomeres and highest order interphase euchromatic DNP structure seem to be correlated with genes that need to be transcribed only under certain developmental conditions. It is proposed that the function of high order structure is to sequester genetic material, namely mainly controller sequences. Since such high order structure, in most cases, would be built up to house the controller dependencies of just one structural gene, the amount of DNA per structural gene needed for gene control would be considerable, and the concept, if correct, would go a long way towards explaining the c-value paradox ("excess" DNA in eukaryotes). In eurygenic determination, the high order structure is thought to be conditioned for melting or to actually melt to an intermediate level of structure. From there, stenogenic control, leading to transcription, is considered to carry the melting process further to yet lower structural levels...
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Surrey S, Nemer M. Methylated blocked 5' terminal sequences of sea urchin embryo messenger RNA classes containing and lacking poly(A). Cell 1976; 9:589-95. [PMID: 1009578 DOI: 10.1016/0092-8674(76)90041-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Sea urchin embryo mRNAs of three distinct classes--histone mRNA, nonhistone mRNA containing poly(A), "[+A] mRNA," and nonhistone mRNA lacking poly(A), "[-A]mRNA"--all contain blocked 5' terminal sequences in which 7-methylguanosine is linked 5'-5' via a triphosphate bridge to a 2'-0-methylated nucleotide. Only one general type of 5' terminal structure, 7mGpppXmpYp, is present. Additional 2'-0-methylation in the Y residue has not been found either in early or late stage embryos. A substantial proportion of the polyribosomal mRNAs in all three classes contain this blocked structure. Whereas both classes of nonhistone mRNAs have internal base methylations, histone mRNAs lack such modifications.
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