Doublet frequency analysis of fractionated vertebrate nuclear DNA

Russell, G. J.; Walker, Peter; Elton, R. A.; Subak‐Sharpe, J. H.

doi:10.1016/s0022-2836(76)80090-3

Cited by 168 publications

(83 citation statements)

References 51 publications

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“…Analysis of the nucleotide sequence reveals that the dinucleotide CpG is infrequently found in influenza virus segment 7, which is similar to the observation that the dinucleotide dCpdG has been found to be deficient in the genome of eukaryotic cells (Russell et al, 1976). It has been suggested that the low frequency of dCpdG in DNA may be related to methylation of cytidine and thus modification of protein-DNA interactions (Razin & Riggs, 1980).…”

supporting

confidence: 61%

Nucleotide Sequence of Fowl Plague Virus RNA Segment 7

McCauley

Mahy

Inglis

1982

Journal of General Virology

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supporting

confidence: 61%

Nucleotide Sequence of Fowl Plague Virus RNA Segment 7

McCauley

Mahy

Inglis

1982

Journal of General Virology

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“…The occurrence of 5-methylcytosine is indeed so low that one might postulate a significant shortage of the doublet C-G in calf thymus DNA. Such a shortage of the doublet C-G has been demonstrated in guinea pig and mouse satellites and even more extreme in bulk vertebrate DNAs [23].…”

Section: Purfication Of Satellite Dnasmentioning

confidence: 93%

Analysis of Calf‐Thymus Satellite DNA: Evidence for Specific Methylation of Cytosine in C‐G Sequences

Gautier¹,

Bûnemann

Grotjahn³

1977

European Journal of Biochemistry

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Digestion of purified calf tymus satellite I (θ= 1.714 g/cm3) with a series of restriction enzymes shows that modification in this satellite occurs preferentially in the sequence C‐G. This was also shown to be the case in the other satellites and in bulk chromosomal calf thymus DNA. Cloning of purified satellite I DNA in Escherichia coli makes sites, previously modified, available for cutting with certain restriction enzymes. All these ‘new’ sites contain the sequence C‐G. High‐resolution mass spectroscopy establishes that the satellites contain a low concentration of 5‐methylcytosine. This iners that methylation which inhibits restriction enzyme cutting must occur preferentially in the sequence C‐G. Hybridization of cRNA of cloned satellite I DNA with the satellites III (θ= 1.706 g/cm3) and IV (θ= 1.710 g/cm3) shows that there is no or little sequence homology between these satellites. Digestion of calf thymus satellite I DNA with endoR ·EcoRI and subsequent hybridization studies with the fragments shows two EcoRI fragments in addition to the usual 1400‐base‐pair EcoRI repeat unit.

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“…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%

“…Biochemical experiments measuring nearest-neighbor frequencies have established that the set of dinucleotide biases is a remarkably stable property of the DNA of an organism (e.g., 10,12). An assessment of the genomic difference between two sequences f and g from different organisms (or from different regions of the same genome) is the average dinucleotide absolute relative-abundance difference calculated as…”

mentioning

confidence: 99%