Nearest Neighbour Base Sequence Analysis of the Deoxyribonucleic Acids of a Further Three Mammalian Viruses: Simian Virus 40, Human Papilloma Virus and Adenovirus Type 2

Morrison, J. M.; Keir, Hamish M.; Subak-Sharpe, H.; Crawford, L. V.

doi:10.1099/0022-1317-1-1-101

Cited by 48 publications

(12 citation statements)

References 8 publications

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“…In view of the obvious clustering of many HhaI and HpaII sites within the viral DNA around the beginning of the putative early gene region, it seemed likely to us that this also reflected a clustering of CG dinucleotides in that particular area of the genome. It has already been noted (14) that CG dinucleotides are statistically underrepresented in the HPV-la genome, and this apparently is a general feature of plant and animal cell DNA (25) as well as the small DNA viruses of mammals (26,27). The HPV-la genome contains 153 CG dinucleotides and their distribution is shown in 8856 -'-1-1-.…”

Section: Distribution Of Cg Dinucleotides Within the Viral Gencmementioning

confidence: 93%

Uneven distribution of methylation sites within the human papillomavirus la genome: possible relevance to viral gene expression

Burnett

Sleeman

1984

Nucl Acids Res

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A homogeneous preparation of human papillomavirus type 1a (HPV-1a) DNA resisted complete cleavage by the methylation-sensitive restriction endonuclease HhaI. Ten fragments additional to those predicted from the known HPV-1a DNA sequence were resolved by agarose gel electrophoresis of the HhaI-cleaved viral DNA. By determining the composite structures of the additional HhaI viral fragments, evidence was found for part-methylation of six of the thirteen HhaI sites. Two of the modified HhaI sites were localized to the 3'-end of the putative early gene region. The other four modified Hha-I sites were situated within the L1 open reading frame of the putative late gene region. Ten successive restriction endonuclease sites occurring close to and within an area of high CG density which surrounds the 5' end of the putative early gene region, were not modified detectably. The possible relevance of DNA methylation to the control of HPV-1a gene expression in epidermal cells is discussed.

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Section: Distribution Of Cg Dinucleotides Within the Viral Gencmementioning

confidence: 93%

Uneven distribution of methylation sites within the human papillomavirus la genome: possible relevance to viral gene expression

Burnett

Sleeman

1984

Nucl Acids Res

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“…It was shown with few exceptions that small eukaryotic viral genomes (Յ30-kb genome size) are CpG suppressed (significantly underrepresented), generally to the same extent as the host genome (8,9,15,16). Small plant viruses are also inclined to be CpG suppressed.…”

Section: E Coli)mentioning

confidence: 99%

“…For double-stranded DNA sequences, a symmetrized version { * XY } is calculated from frequencies of the sequence concatenated with its inverted complementary sequence. Our studies of DNA and genomic data have demonstrated that the dinucleotide relative abundance profiles { * XY } evaluated for disjoint 50-kb DNA contigs from the same organism are approximately constant throughout its genome and are generally more congruent to each other than they are to those from 50-kb contigs of different organisms (8)(9)(10)(11)(12). On this basis, we refer to the vector profile { * XY } of a given genome as its ''genomic signature'' diagnostic of different groups of organisms.…”

mentioning

confidence: 99%

Distinctive features of large complex virus genomes and proteomes

Mrázek

Karlin

2007

Proc. Natl. Acad. Sci. U.S.A.

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“…It is well known that the dCpdG sequence is remarkably low in vertebrate DNA and in many animal DNA viruses [51,52]. The single dCpdG which does occur in the Hind-K DNA is in the region of the gene overlap (vide infia) and there- A-A-A, G-G-A.…”

Section: Discussionmentioning

confidence: 99%

Nucleotide Sequence of the Simian Virus 40 Hind‐K Restriction Fragment

Rogiers¹,

Voorde²,

Soeda

et al. 1978

European Journal of Biochemistry

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The restriction fragment Hind-K represents 4.2 ' %, of the genome of Simian virus 40 (SV40) and is located near the middle of the late region. Tts nucleotide sequence is reported here. It was mainly established by analysis of transcription products, synthesized by means of Esscherichiu coli RNA polymerase and nucleoside triphosphates, one of which was (~-~~P ) -l a b e l e d .Strand assignment was possible by hybridization of asymmetric, labeled transcripts of total SV40 DNA to filter-bound Hind-K fragment. Further information and unambiguous confirmation of the sequence was obtained by the use of direct DNA-sequencing methods. For this purpose the fragment was labeled at the 5' ends by means of polynucleotide kinase and [ Y -~~P I A T P and redigested with a suitable restriction enzyme. The separated products were then either partially digested with snake venom diesterase for analysis by the 'wandering spot' method or partially degraded with the base-specific reagents dimethylsulphate or hydrazine for direct sequence analysis on gel. The Hind-K sequence is 219 base pairs long. The message strand is particularly rich in adenosine (39 2) and purines. The nucleotide sequence can unambiguously be translated into an amino acid sequence and the N-terminal codon of the viral protein VP1 gene could be identified. The amino-terminal part of VP1 is rich in proline and lysine. The nucleotide sequence of Hind-K codes also for the carboxylterminal part of the viral protein VP2 and VP3 genes, which partly overlap the VP1 gene.In order to understand the organization of the genetic information in the oncogenic animal virus Simian virus 40 (SV40) in molecular detail, we have sequenced various parts of this genome. The viral DNA is a circular, double-stranded, supercoiled molecule containing approximately 5200 base pairs. It is cleaved by the HzndII+III restriction endonucleases into 13 fragments which were ordered [1,2]

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Nearest Neighbour Base Sequence Analysis of the Deoxyribonucleic Acids of a Further Three Mammalian Viruses: Simian Virus 40, Human Papilloma Virus and Adenovirus Type 2

Cited by 48 publications

References 8 publications

Uneven distribution of methylation sites within the human papillomavirus la genome: possible relevance to viral gene expression

Uneven distribution of methylation sites within the human papillomavirus la genome: possible relevance to viral gene expression

Distinctive features of large complex virus genomes and proteomes

Nucleotide Sequence of the Simian Virus 40 Hind‐K Restriction Fragment

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