201
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Efstratiadis A, Posakony JW, Maniatis T, Lawn RM, O'Connell C, Spritz RA, DeRiel JK, Forget BG, Weissman SM, Slightom JL, Blechl AE, Smithies O, Baralle FE, Shoulders CC, Proudfoot NJ. The structure and evolution of the human beta-globin gene family. Cell 1980; 21:653-68. [PMID: 6985477 DOI: 10.1016/0092-8674(80)90429-8] [Citation(s) in RCA: 1171] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We present the results of a detailed comparison of the primary structure of human beta-like globin genes and their flanking sequences. Among the sequences located 5' to these genes are two highly conserved regions which include the sequences ATA and CCAAT located 31 +/- 1 and 77 +/- 10 bp, respectively, 5' to the mRNA capping site. Similar sequences are found in the corresponding locations in most other eucaryotic structural genes. Calculation of the divergence times of individual beta-like globin gene pairs provides the first description of the evolutionary relationships within a gene family based entirely on direct nucleotide sequence comparisons. In addition, the evolutionary relationship of the embryonic epsilon-globin gene to the other human beta-like globin genes is defined for the first time. Finally, we describe a model for the involvement of short direct repeat sequences in the generation of deletions in the noncoding and coding regions of beta-like globin genes during evolution.
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202
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Abstract
We present the complete nucleotide sequence of the human delta-globin gene. The general DNA sequence organization of the delta-globin gene is similar to that of other known globin genes. We have been unable to identify unambiguously the structural basis of the low level of expression characteristic of the delta-globin gene.
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203
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Wilson JT, Wilson LB, Reddy VB, Cavallesco C, Ghosh PK, deRiel JK, Forget BG, Weissman SM. Nucleotide sequence of the coding portion of human alpha globin messenger RNA. J Biol Chem 1980; 255:2807-15. [PMID: 6244294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequence of the coding portion of human alpha globin mRNA has been determined by sequence analysis using human alpha globin cDNA cloned in bacterial plasmids. The sequence was obtained by a combination of direct sequence analysis of the cloned cDNA and analysis of cDNA obtained by primer extension, using short restriction endonuclease fragments of cloned alpha cDNA that were hybridized to human globin mRNA and elongated on the mRNA template by viral reverse transcriptase. The human alpha globin mRNA has an unexpectedly high G + C base composition (64.7%), similar to that observed for rabbit globin alpha mRNA, and displays a striking bias in the use of synonym codons for various amino acids. The bias in codon usage of human alpha globin mRNA is similar, with some exceptions, to that previously observed for rabbit alpha globin mRNA as well as for human and rabbit beta globin mRNAs. A detailed restriction endonuclease map of the human alpha globin cDNA is presented.
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204
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Forget BG, Marotta CA, Cohen-Solal M, Wilson JT, Weissman SM. Partial nucleotide sequence of human alpha globin mRNA derived from analysis of 32P-labeled cRNA and 125I-labeled mRNA; correlation with a globin cDNA sequence. J Biol Chem 1980; 255:2814-5. [PMID: 7358710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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205
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Jelinek WR, Toomey TP, Leinwand L, Duncan CH, Biro PA, Choudary PV, Weissman SM, Rubin CM, Houck CM, Deininger PL, Schmid CW. Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci U S A 1980; 77:1398-402. [PMID: 6246492 PMCID: PMC348502 DOI: 10.1073/pnas.77.3.1398] [Citation(s) in RCA: 450] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
DNA base sequence comparisons demonstrate that the principal family of 300-nucleotide interspersed human DNA sequences, the repetitive double-strand regions of HeLa cell heterogeneous nuclear RNA, and specific RNA polymerase III in vitro transcripts of cloned human DNA sequences are all representatives of a closely related family of sequences. A segment of approximately 30 residues of these sequences is highly conserved in mammalian evolution because it is also present in the interspersed repeated DNA sequences of Chinese hamsters. Further DNA sequence comparisons demonstrate that a portion of this highly conserved segment of repetitive mamalian DNA sequence is similar to a sequence found within a low molecular weight RNA that hydrogen-bonds to poly(A)-terminated RNA molecules of Chinese hamsters and a sequence that forms half of a perfect inverted repeat near the origin of DNA replication in papovaviruses.
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206
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Ghosh PK, Reddy VB, Piatak M, Lebowitz P, Weissman SM. Determination of RNA sequences by primer directed synthesis and sequencing of their cDNA transcripts. Methods Enzymol 1980; 65:580-95. [PMID: 6154870 DOI: 10.1016/s0076-6879(80)65061-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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207
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Ghosh PK, Piatak M, Reddy VB, Swinscoe J, Lebowitz P, Weissman SM. Transcription of the SV40 genome in virus-transformed cells and early lytic infection. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1980; 44 Pt 1,:31-9. [PMID: 6159134 DOI: 10.1101/sqb.1980.044.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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208
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Duncan C, Biro PA, Choudary PV, Elder JT, Wang RR, Forget BG, de Riel JK, Weissman SM. RNA polymerase III transcriptional units are interspersed among human non-alpha-globin genes. Proc Natl Acad Sci U S A 1979; 76:5095-9. [PMID: 388428 PMCID: PMC413086 DOI: 10.1073/pnas.76.10.5095] [Citation(s) in RCA: 118] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cloned human DNA fragments containing globin genes are transcribed in vitro to form discrete RNA species. One transcription unit is located approximately 1500 base pairs upstream from the G-gamma-globin gene. This transcript is partially homologous to a polymerase III template located approximately 1000 base pairs upstream from the delta-globin gene and to DNA located a short distance downstream from the beta-globin gene.
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209
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210
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Reddy VB, Ghosh PK, Lebowitz P, Piatak M, Weissman SM. Simian virus 40 early mRNA's. I. Genomic localization of 3' and 5' termini and two major splices in mRNA from transformed and lytically infected cells. J Virol 1979; 30:279-96. [PMID: 90157 PMCID: PMC353322 DOI: 10.1128/jvi.30.1.279-296.1979] [Citation(s) in RCA: 189] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We have studied the structure of polyadenylated virus-specific cytoplasmic mRNA's in mouse and human cells transformed by simian virus 40 and in monkey cells infected with simian virus 40 in the presence of cytosine arabinoside by means of reverse transcriptase-catalyzed complementary DNA synthesis and complementary DNA sequencing. Abundant mRNA species containing splices from residues 4490 to 4557 (0.533 to 0.546 map units [m.u.]) and 4490 to 4837 (0.533 to 0.600 m.u.) were identified in both transformed and infected cells. Two principal reverse transcriptase stops were observed at the 5' termini of these mRNA's, both occurring with approximately equal frequency. The most distal of these stops was localized at residues 5152 to 5154 (0.660 m.u.), and the second was at residues 5147 to 5148 (0.659 m.u.). Several additional minor stops, between approximately 0.62 and 0.65 m.u., were also found on complementary DNA copied from transformed cell mRNA; in contrast, only one additional stop was present on complementary DNA copied from early lytic mRNA. These data suggest the presence of a prinicipal 5' terminus of early lytic and transformed cell mRNA's at residues 5152 to 5154 and raise the possibility of additional 5' termini at one or more locations in the 0.62 to 0.659 m.u. region of these mRNA's. Transformed cell mRNA was also found to contain a single 3' terminus at positions 2504 and 2505 (0.153 m.u.); termini lying beyond this site were not detected.
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211
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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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212
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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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213
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Reddy VB, Ghosh PK, Lebowitz P, Weissman SM. Gaps and duplicated sequences in the leaders of SV40 16S RNA. Nucleic Acids Res 1978; 5:4195-213. [PMID: 82936 PMCID: PMC342743 DOI: 10.1093/nar/5.11.4195] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In order to investigate the 5' terminal structural heterogeneity of the 16S size class of SV40 late RNA, we have bound an SV40 DNA fragment labeled at its 5' termini with P32 to the .939-.945 map unit region of late lytic cytoplasmic polyadenylated RNA, used reverse transcriptase to prepare cDNA copies of the 5' termini of this RNA, separated the cDNA products on an 8% polyacrylamide-7 M urea gel and subjected these products to nucleic acid sequence analysis. A number of discrete cDNAs were obtained. Analysis of these cDNAs has suggested the presence of three categories of 16S species all containing the same body extending from residues 1381-2592 (.939-.170 m.u.) but differring in the structure of their leader segments. Members of the first category contain leaders which are colinear with SV40 DNA, have a common 3' terminus at residue 444 and extend varying distances in a 5' direction. The most abundant 16S species contains a leader of 203 nucleotides and is a member of this group. RNAs of the second category contain leaders with an internal gap between residues 211-352. The single RNA comprising the third category contains a leader with a tandem repetition of nucleotides 351-443 at the 3' terminus of its leader.
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214
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Ghosh PK, Reddy VB, Swinscoe J, Choudary PV, Lebowitz P, Weissman SM. The 5'-terminal leader sequence of late 16 S mRNA from cells infected with simian virus 40. J Biol Chem 1978; 253:3643-7. [PMID: 206548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 16 S mRNA that directs the synthesis of VP1, the major structural protein of Simian virus 40 (SV40), is composed of a leader sequence of 203 nucleotides joined to a transcript that contains all the codons for VP1. The leader is transcribed from DNA between 0.723 and 0.762 map units while the VP1 coding transcript is copied from DNA from 0.94 to 0.17 map units. The leader sequence joins the transcript of the coding region at a position 42 nucleotides upstream from the initiator codon for VP1 by a 3':5'-phosphodiester linkage. Longer leader sequences also occur in a portion of SV40 late mRNA.
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215
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Reddy VB, Thimmappaya B, Dhar R, Subramanian KN, Zain BS, Pan J, Ghosh PK, Celma ML, Weissman SM. The genome of simian virus 40. Science 1978; 200:494-502. [PMID: 205947 DOI: 10.1126/science.205947] [Citation(s) in RCA: 852] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The nucleotide sequence of SV40 DNA was determined, and the sequence was correlated with known genes of the virus and with the structure of viral messenger RNA's. There is a limited overlap of the coding regions for structural proteins and a complex pattern of leader sequences at the 5' end of late messenger RNA. The sequence of the early region is consistent with recent proposals that the large early polypeptide of SV40 is encoded in noncontinguous segments of DNA.
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216
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Zain BS, Thimmappaya B, Dhar R, Weissman SM. Nucleotide sequences of DNA encoding the 3' ends of SV40 mRNA. I. The sequence of the DNA fragment Hi-DII,III-G. J Biol Chem 1978; 253:1606-12. [PMID: 203596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 3' ends of the mRNA coding for the early and late proteins of SV40 DNA overlap. We have analyzed the restriction endonuclease fragment of SV40 DNA complementary to the 3' untranslated ends of the mRNA and the codons for the COOH-terminal amino acids of early and late protein. The sequence of this DNA fragment is presented.
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217
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Thimmappaya B, Zain BS, Dhar R, Weissman SM. Nucleotide sequence of DNA template for the 3' ends of SV40 mRNA. II. The sequence of the DNA fragment EcorII-F and a part of EcorII-H. J Biol Chem 1978; 253:1613-8. [PMID: 203597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nucleotide sequence for two-thirds of restriction endonuclease fragment EcoRII-F and part of RII-H of SV40 DNA is presented. This segment of SV40 DNA is complementary to the sequence near the 3' end of early mRNA. This sequence could be translated in one reading frame to form a large protein. However, in a second translational frame there are four AUG codons followed by 91 sense triplets, followed by a termination codon. These results provide the sequence for the entire 3' untranslated ends of SV40 early and late mRNAs and for the DNA beyond the 3' ends of the mRNAs. The ends of early and late mRNA are transcribed from the opposite strands of the same segment of DNA. At or beyond the 3' ends of both early and late mRNA are sequences whose transcripts would include uridylic acid-rich products.
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218
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Wilson JT, Wilson LB, deRiel JK, Villa-komaroff L, Efstratiadis A, Forget BG, Weissman SM. Insertion of synthetic copies of human globin genes into bacterial plasmids. Nucleic Acids Res 1978; 5:563-81. [PMID: 345245 PMCID: PMC342002 DOI: 10.1093/nar/5.2.563] [Citation(s) in RCA: 284] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Double stranded human globin cDNA was synthesized by use of viral reverse transcriptase from globin mRNA of cord blood of premature infants requiring exchange transfusions. The cDNA was introduced into plasmids and the recombinant DNA plasmids used to transform E. coli X1776. A number of transformants were obtained. Plasmid DNA from selected colonies was isolated and characterized for the type of globin cDNA it contained by three types of procedures: 1) hybridization to previously characterized 3H-labeled alpha,beta and gamma cDNA; 2) analysis of the size and nature of fragments produced by digestion of the plasma DNA by different restriction endonucleases; and 3) by rapid DNA sequence analysis of selected DNA fragments produced by restriction endonuclease digestion. Analysis by these techniques of plasmid DNA from different colonies has definitively identified the presence of human alpha, beta or gamma cDNA sequences in different plasmids.
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219
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Dhar R, Reddy VB, Weissman SM. Nucleotide sequence of the DNA encoding the 5'-terminal sequences of simian virus 40 late mRNA. J Biol Chem 1978; 253:612-20. [PMID: 201640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have used a combination of techniques of DNA and RNA sequence analysis to determine the nucleotide sequence of the portion of simian virus 40 DNA preceding and encoding the 5' end of mRNA for the structural protein VP2 of simian virus 40. Comparison of the sequence with those found in polyadenylated RNA in the cytoplasm of infected cells RNA shows that the transcript of sequences preceding the structural gene is more abundant than the transcript containing the codons for the protein. Between the abundant transcript of sequences preceding the coding region and the less abundant transcript of the coding region there is a short sequence whose transcript is not detected.
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220
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Reddy VB, Dhar R, Weissman SM. Nucleotides sequence of the genes for the simian virus 40 proteins VP2 and VP3. J Biol Chem 1978; 253:621-30. [PMID: 201641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have determined the nucleotide sequence of the DNA of simian virus 40. The proceeding report (Dhar, R., Reddy, V.B., and Weissman, S.M. (1978) J. Biol. Chem. 253, 612-620) presents the sequence of a portion of the simian virus 40 DNA that overlaps the region encoding the 5' end of the minor structural protein VP2. We report here the sequence of the remainder of the genes for minor structural proteins VP2 and VP3. The results indicate that the mRNA for the two proteins is read in the same phase and the initiation site for VP3 lies within the structural gene of VP2. The codons of the COOH-terminal amino acids of VP2 and VP3 are read in a second phase as the codons of the NH2-terminal amino acids of VP1.
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221
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Thimmappaya B, Reddy VB, Dhar R, Celma M, Subramanian KN, Zain BS, Pan J, Weissman SM. The structure of genes, intergenic sequences, and mRNA from SV40 virus. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1978; 42 Pt 1:449-56. [PMID: 209943 DOI: 10.1101/sqb.1978.042.01.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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222
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Pan J, Celma ML, Weissman SM. Studies of low molecular weight RNA from cells infected with adenovirus 2. III. The sequence of the promoter for VA-RNA I. J Biol Chem 1977; 252:9047-54. [PMID: 200627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
VA-RNA I is one of the very few RNA species produced in animal cells whose transcriptional initiation site is known precisely. We have analyzed the nucleotide sequence of the DNA preceding the 5' end of VA-RNA I and compared it with known prokaryotic promoters and presumptive eukaryotic promoters.
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223
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Celma ML, Pan J, Weissman SM. Studies of low molecular weight RNA from cells infected with adenovirus 2. I. The sequences at the 3' end of VA-RNA I. J Biol Chem 1977; 252:9032-42. [PMID: 318160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
VA-RNA I is a low molecular weight RNA produced in large amounts in cells infected with adenoviruses. The 3' terminus of this RNA may represent a transcription termination site. We have demonstrated that this RNA occurs in infected cells in several forms which differ in the number of uridylic acid residues at the 3' ends. The nucleotide sequence of a DNA fragment overlapping the 3' end of VA-RNA I has been determined. The DNA could encode up to 4 uridylic acid residues at the 3' end of the RNA. The DNA sequence shows some similarity to known transcription termination sequences in prokaryotic systems.
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224
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Celma ML, Pan J, Weissman SM. 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; 252:9043-6. [PMID: 925035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The 5'-terminal sequences of VA-RNA I produced in cells infected with adenovirus 2 were analyzed. The RNA contained a mixture of mono-, di-, and triphosphate ends. The largest part of the RNA has 5'-terminal mono-, di-, or triphosphoguanylic acid, but a portion of the RNA has a 5'-terminal mono-, di-, or triphosphoadenylic acid. An RNA with 5'-terminal adenylic acid was purified and gave the same oligonucleotide map as the major form of VA-RNA I, except for the 5'-terminal products. We therefore conclude that transcription of VA-RNA I can initiate at two different nearby sites.
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225
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Kafatos FC, Efstratiadis A, Forget BG, Weissman SM. Molecular evolution of human and rabbit beta-globin mRNAs. Proc Natl Acad Sci U S A 1977; 74:5618-22. [PMID: 271989 PMCID: PMC431834 DOI: 10.1073/pnas.74.12.5618] [Citation(s) in RCA: 134] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The primary structures of human and rabbit beta-globin mRNAs are compared. Using as a standard the extent of nucleotide substitutions inferred from the hypervariable amino acid residues of fibrinopeptides A and B, which are thought to change largely by neutral evolution, we show that not all silent mutations in globin mRNA are neutral. The divergence of the sequences is limited in part by the selective usage of synonymous codons. The divergent nucleotides tend to be distributed nonrandomly: in the coding region silent substitutions are most rare in segments that are also deficient in substitutions leading to replacements.
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226
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Pan J, Reddy VB, Thimmappaya B, Weissman SM. Nucleotide sequence of the gene for the major structural protein of SV40 virus. Nucleic Acids Res 1977; 4:2539-48. [PMID: 198745 PMCID: PMC342590 DOI: 10.1093/nar/4.8.2539] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have determined the sequence of the portion of Simian Virus 40 (SV40) that codes for the major structural protein of the virus. The gene contains 361 codons. Synonym codons for an amino acid are not used randomly. The dinucleotide CG occurs only once and there is 2 to 1 preference for uridylic acid in the third position of codons.
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227
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Abstract
The nucleotide sequence of 70 base pairs (bp) around 0.545 map units (Alu I C and B junction) of the genome from the single Eco RI cleavage site within SV40 DNA is presented. The mRNA transcribed from the early strand template from this stretch contains two copies of the nonsense triplet UAA in each of the three reading frames. Thus at least 25% of the early region of SV40 DNA does not code for the SV40 "A" protein, and the viral contribution to events in the lytic cycle and transformation may be more complex than is generally appreciated.
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228
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Celma ML, Dhar R, Pan J, Weissman SM. Comparison of the nucleotide sequence of the messenger RNA for the major structural protein of SV40 with the DNA sequence encoding the amino acids of the protein. Nucleic Acids Res 1977; 4:2549-50. [PMID: 198746 PMCID: PMC342591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 16S late mRNA from SV40 directs the synthesis of the major viral structural protein, VP1. We have compared the oligonucleotides in the 16S mRNA with those that would be present in a transcript of the portion of SV40 DNA coding for VP1. The results indicate that a segment of about 200 nucleotides of RNA transcribed from a distant part of SV40 DNA have become linked to the transcript of VP1 codons by a bond resistant to phenol extraction and denaturation in formamide.
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229
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Marotta CA, Wilson JT, Forget BG, Weissman SM. Human beta-globin messenger RNA. III. Nucleotide sequences derived from complementary DNA. J Biol Chem 1977; 252:5040-53. [PMID: 68958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sequences of human beta-globin mRNA were determined by analysis of complementary DNA. beta-mRNA was transcribed into double-stranded cDNA by RNA-dependent DNA polymerase. cDNA was cut by restriction endonucleases and the fragments were terminally labeled by means of polynucleotide kinase and [gamma-32P]ATP. After purification, fragments were degraded by snake venom phosphodiesterase. Alternatively single-stranded [32P]cDNA was prepared by transcription in the presence of [alpha-32P]dCTP and actinomycin D; the product was digested by endonuclease IV and degraded by snake venom phosphodiesterase. cDNA tracts obtained by both labeling methods enabled us to construct a sequence for the translated and 3'-terminal untranslated regions of human beta-mRNA.
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230
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Marotta CA, Forget BG, Cohne-Solal M, Wilson JT, Weissman SM. Human beta-globin messenger RNA. I. Nucleotide sequences derived from complementary RNA. J Biol Chem 1977; 252:5019-31. [PMID: 873928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Sequence analysis studies were carried out on human beta-globin mRNA (beta-mRNA) prepared from alpha-thalassemic, sickle cell, and Hb A reticulocytes. Highly purified beta-mRNA served as substrate for the preparation of cDNA by RNA-dependent DNA polymerase. The cDNA was transcribed by Escherichia coli RNA polymerase and the resulting cRNA was analyzed. Over 300 nucleotides were assigned to the beta-mRNA coding region and 37 nucleotides were assigned to the 3'-terminal noncoding region. The normal termination codon is UAA which is separated by 28 nucleotides from an out of phase UAA triplet. The origin of each of the abnormally long beta-globin variants Tak and Cranston is consistent with reduplication of dinucleotides prior to the normal termination codon, and both globin variants can terminate at the out of phase UAA.
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231
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Cohen-Solal M, Forget BG, Prensky W, Marotta CA, Weissman SM. Human beta-globin messenger RNA. II. nucleotide sequences derived from 125I-labeled globin messenger RNA. J Biol Chem 1977; 252:5032-9. [PMID: 318159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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232
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Wilson JT, deRiel JK, Forget BG, Marotta CA, Weissman SM. Nucleotide sequence of 3' untranslated portion of human alpha globin mRNA. Nucleic Acids Res 1977; 4:2353-68. [PMID: 909779 PMCID: PMC342571 DOI: 10.1093/nar/4.7.2353] [Citation(s) in RCA: 39] [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
We have determined the nucleotide sequence of 75 nucleotides of the 3'-untranslated portion of normal human alpha globin mRNA which corresponds to the elongated amino acid sequence of the chain termination mutant Hb Constant Spring. This was accomplished by sequence analysis of cDNA fragments obtained by restriction endonuclease or T4 endonuclease IV cleavage of human globin cDNA synthesized from globin mRNA by use of viral reverse transcriptase. Analysis of cRNA synthesized from cDNA by use of RNA polymerase provided additional confirmatory sequence information. Possible polymorphism has been identified at one site of the sequence. Our sequence overlaps with, and extends the sequence of 43 nucleotides determined by Proudfood and coworkers for the very 3'-terminal portion of human alpha globin mRNA. The complete 3'-untranslated sequence of human alpha globin mRNA (112 nucleotides including termination codon) shows little homology to that of the human or rabbit beta globin mRNAs except for the presence of the hexanucleotide sequence AAUAAA which is found in most eukaryotic mRNAs near the 3'-terminal poly (A).
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233
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Cohen-Solal M, Forget BG, Prensky W, Marotta CA, Weissman SM. Human beta-globin messenger RNA. II. nucleotide sequences derived from 125I-labeled globin messenger RNA. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40155-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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234
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Lebowitz P, Stern R, Ghosh PK, Weissman SM. Specificity of initiation of transcription of simian virus 40 DNA I by Escherichia coli RNA polymerase: identification and localization of five sites for initiation with [gamma-32P]ATP. J Virol 1977; 22:430-45. [PMID: 194061 PMCID: PMC515734 DOI: 10.1128/jvi.22.2.430-445.1977] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Simian virus 40 (SV40) DNA I was transcribed with Escherichia coli RNA polymerase in the presence of gamma-32P-labeled ribonucleoside triphosphates in order to investigate the specificity of initiation of in vitro transcription. ATP and GTP served as predominant initiating nucleotides, the former being incorporated about twice as much as the latter. Cleavage of [gamma-32P]ATP-labeled SV40 complementary RNA (cRNA) with T1 RNase followed by homochromatographic analysis of the resultant 5' initiation fragments revealed the presence of four specific initiation fragments 6 to 9 nucleotides in length, designated AI, AII, AIIIa, and AIIIb. By means of hybridization of [gamma-32P]ATP-labeled SV40 cRNA to DNA from specific adenovirus 2-SV40 hybrids and specific restriction endonuclease fragments of SV40 DNA before chromatographic analysis, it was possible to identify and determine approximate localizations of five [gamma-32P]ATP initiation sites on the SV40 genome: one in Hin-G close to the Hin-G-B junction, giving rise to the AII fragment, two in the overalpping fragment Hin-A-Hae-A,giving rise to AI and AIII fragments, and two in the fragment Hin-A-Hae-E, also giving rise to AI and AIII fragments. All five sites either fall within or lie near regions of the genome that are cleaved by S1 nuclease and subject to partial alkaline denaturation. These five sites lie on the minus strand of SV40 DNA and initiate RNAs that are copied in a leftward direction. Cleavage of [gamma-32P]GTP-labeled cRNA with pancreatic RNase liberated three major 5' initiation fragments of short length, GI, GII, and GIII, suggesting the presence of three principal GTP initiation sites.
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235
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Wilson JT, Forget BG, Wilson LB, Weissman SM. Human globin messenger RNA: importance of cloning for structural analysis. Science 1977; 196:200-2. [PMID: 847468 DOI: 10.1126/science.847468] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The sequence of most of the human beta globin messenger RNA and large sections of the alpha globin messenger RNA has been determined. Partly because of genetic polymorphism, it was necessary to clone globin complementary DNA in order to extend the analysis. Purified human fetal globin messenger RNA was isolated and used as a template by reverse transcriptase to produce duplex complementary DNA molecules. These molecules were linked in vitro to plasmid DNA by use of T4 ligase in the presence of Escherichia coli Pol 1. Several colonies transformed by these molecules have been shown to hybridize with labeled human globin complementary RNA.
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Dhar R, Subramanian KN, Pan J, Weissman SM. Structure of a large segment of the genome of simian virus 40 that does not encode known proteins. Proc Natl Acad Sci U S A 1977; 74:827-31. [PMID: 191835 PMCID: PMC430491 DOI: 10.1073/pnas.74.3.827] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nucleotide sequence of the region of DNA of simian virus 40 extending from 0.595 to 0.790 map unit has been derived. The sequence includes the DNA complementary to the 5' end of early mRNA and to the 5' end of some of the forms of late RNA. Because there are termination codons in all three phases in early and late RNA, there is a sequence of almost 800 nucleotides of simian virus 40 DNA that probably does not code for known viral proteins. The sequence spans the 5' end of the early mRNA at 0.67 map unit and overlaps a species of late RNA whose 5' end is at 0.65 map unit and whose 3' end is at 0.77 map unit. This RNA is retained on oligo(dT)-cellulose columns in high salt concentrations. Analysis of the sequence of late strand RNA suggests that this RNA is not covalently linked to the mRNA that encodes structural proteins. There is another species of late RNA of simian virus 40 whose 5' end is at 0.775 map unit. The nucleotide sequence of this region of simian virus 40 DNA contains several examples of repeated sequences, most of which are located in DNA that does not encode known peptides. These may be analogous to the reiterated sequences that have been described in animal cell DNA.
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237
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Subramanian KN, Reddy VB, Weissman SM. Occurrence of reiterated sequences in an untranslated region of Simian virus 40 DNA determined by nucleotide sequence analysis. Cell 1977; 10:497-507. [PMID: 191198 DOI: 10.1016/0092-8674(77)90037-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An earlier report (Subramanian, Dhar, and Weissman, 1977c) presented the nucleotide sequence of Eco RII-G fragment of SV40 DNA, which contains the origin of DNA replication. The nucleotide sequence of Eco RII-N fragment located next to Eco RII-G on the physical map of SV40 DNA is presented in this report. Eco RII-N is found to be a tandem duplication of the last 55 nucleotides of Eco RII-G. This tandem repeat is immediately preceded by two other reiterated sequences occurring within Eco RII-G, one of them being a tandem repeat of 21 nucleotides and the other a nontandem repeat of 10 nucleotides. These repetitive sequences occur in close proximity to the origin of DNA replication which is known to contain other specialized sequences such as a few palindromes (one of which is 27 long and possesses a perfect 2-fold axis of symmetry), one "true" palindrome, and a long A/T-rich cluster. The repeats (and the replication origin) occur within an untranslated region of SV40 DNA flanked by (the few) structural genes coding for the "late" proteins on the one side and that (those) coding for the "early" protein(s) on the other side. The reiterated sequences are comparable in some respects to repetitive sequences occurring in eucaryotic DNAs. Possible biological functions of the repeats are discussed.
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238
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Subramanian KN, Zain BS, Roberts RJ, Weissman SM. Mapping of the HhaI and HinfI cleavage sites on simian virus 40 DNA. J Mol Biol 1977; 110:297-317. [PMID: 191618 DOI: 10.1016/s0022-2836(77)80074-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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239
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Subramanian KN, Dhar R, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. III. Construction of the total sequence of EcoRII-G fragment of SV40 DNA. J Biol Chem 1977; 252:355-67. [PMID: 188810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Limited T1 RNase digestion of subfragments of the SV40 DNA restriction endonuclease fragment EcoRII-G were prepared and analyzed. The fragments were separately labeled with 32P at their 5' terminus and the terminal sequences analyzed with limited snake venom diesterase digestion. The data permitted us to deduce the nucleotide sequence for EcoRII-G. The sequence contains a stretch of 17 A-T base pairs preceding the DNA complementary to the 5' end of "early" message RNA, a stretch of 27 bases with a perfect 2-fold rotational symmetry near the origin of DNA replication and a perfect tandem repeat of 21 nucleotides.
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240
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Subramanian KN, Dhar R, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. I. Mapping of the restriction endonuclease sites within the EcoRII-G fragment and strategy employed for its sequence analysis. J Biol Chem 1977; 252:333-9. [PMID: 188808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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241
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Dhar R, Subramanian KN, Pan J, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. IV. Localization of the SV40 DNA complementary to the 5' ends of viral mRNA. J Biol Chem 1977; 252:368-76. [PMID: 188811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic mRNA isolated from cells infected with SV40 was isolated by passage over oligo(dT)-cellulose columns. This RNA was annealed to SV40 DNA fragments produced by cleavage with EcoRII endonuclease. The RNA resistant to RNase digestion was analyzed by digestion with ribonucleases and oligonucleotide mapping. The results were compared with oligonucleotides from in vitro transcripts of the fragments and with whole genome SV40 cRNA which had been fractionated by hybridization to the fragments. The 5' ends of "early" and the large "late" SV40 mRNA, transcribed from opposite DNA strands, overlap for a region of 60 to 100 nucleotides. The region of overlap includes a portion of the segment of DNA containing the origin of DNA replication.
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242
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Subramanian KN, Dhar R, Weissman SM, Ghosh PK. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. II. Sequences of T1 and pancreatic ribonuclease digestion products of RNA transcripts prepared from subfragments of EcoRII-G. J Biol Chem 1977; 252:340-54. [PMID: 188809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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243
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Subramanian KN, Dhar R, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. I. Mapping of the restriction endonuclease sites within the EcoRII-G fragment and strategy employed for its sequence analysis. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32835-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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244
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Subramanian KN, Dhar R, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. III. Construction of the total sequence of EcoRII-G fragment of SV40 DNA. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32837-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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245
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Subramanian KN, Dhar R, Weissman SM, Ghosh PK. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. II. Sequences of T1 and pancreatic ribonuclease digestion products of RNA transcripts prepared from subfragments of EcoRII-G. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32836-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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246
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Subramanian KN, Ghosh PK, Dhar R, Thimmappaya B, Zain SB, Pan J, Weissman SM. The primary structure of regions of SV 40 DNA encoding the ends of mRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:157-64. [PMID: 190641 DOI: 10.1016/s0079-6603(08)60916-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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247
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Dhar R, Subramanian KN, Pan J, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. IV. Localization of the SV40 DNA complementary to the 5' ends of viral mRNA. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32838-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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248
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Marotta CA, Forget BG, Cohen-Solal M, Weissman SM. Nucleotide sequence analysis of coding and noncoding regions of human beta-globin mRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:165-75. [PMID: 1019344 DOI: 10.1016/s0079-6603(08)60917-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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249
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Marotta CA, Varricchio F, Smith I, Weissman SM. The primary structure of Bacillus subtilis and Bacillus stearothermophilus 5 S ribonucleic acids. J Biol Chem 1976; 251:3122-7. [PMID: 818086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The nucleotide of Bacillus stearothermophilus 5 S RNA is pC-C-U-A-G-U-G-A-C-A-A-U-A-G-C-G-(G-A-G-A-G-G-)-A-A-A-C-A-C-C-C-G-U-U-C-C-C-A-U-C-C-C-G-A-A-C-A-C-G-G-A-A-G-U-U-A-A-G-C-U-C-U-C-C-A-G-C-G-C-C-G-A-U-G-G-U-A-G-U-U-G-G-G-G-C-C-A-G-C-G-C-C-C-C-U-G-C-A-A-G-A-G-U-A-G-G-U-C-G-U-U-G-C-U-A-G-G-COH; the nucelotide sequence of Bacillus subtilis 5 S RNA is pU-U-U-G-G-U-G-G-C-G-A-U-A-G-C-G-A-A-G-A-G-G-U-C-A-C-A-C-C-C-G-U-U-C-C-C-A-U-A-C-C-G-A-A-C-A-C-G-G-A-A-G-U-U-A-A-G-C-U-C-U-U-C-A-G-C-G-C-C-G-A-U-G-G-U-A-G-U-C-G-G-G-G-G-U-U-U-C-C-C-C-C-U-G-U-G-A-G-A-G-U-A-G-G-A-C-G-C-C-G-C-C-A-A-G-COH. Comparison of the sequence of B. stearothermophilus 5 S RNA to the sequence of B. subtilis 5 S RNA and to that of Bacillus megaterium 5 S RNA (Pribula, C. D., Fox, G. E., Woese, C. R., Sogin, M., and Pace, N. (1974) FEBS Lett. 44, 322-323) indicates that the 5 S RNA isolated from the thermophile contains unique nucleotide sequences not found in 5 S RNAs isolated from the two mesophilic species of genus Bacillus.
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250
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Marotta CA, Varricchio F, Smith I, Weissman SM. The primary structure of Bacillus subtilis and Bacillus stearothermophilus 5 S ribonucleic acids. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33507-x] [Citation(s) in RCA: 16] [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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