Nucleotide sequence comparison of the Adh gene in three drosophilids

Cohn, Vivian H.; Thompson, Margaret A.; Moore, George T.

doi:10.1007/bf02101983

Cited by 51 publications

(24 citation statements)

References 25 publications

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“…We compared the glyceraldehyde-3-phosphate dehydrogenase genes in yeast and C. elegans, two nonmethylated forms, and found that, of 11 CpGs in yeast, a total of 3 (27%) had changed in C. elegans, all to TpG. At the control dinucleotides, 8 (15): there were 46 sites where at least one species had a CpG and only 3 sites (6%) varied between these species. At the control dinucleotides, 9 of 194 sites (5%) varied between these species, which is not significantly different from the frequency of change at the CpG dinucleotides.…”

Section: Resultsmentioning

confidence: 99%

Analysis of CpG suppression in methylated and nonmethylated species.

Schorderet

Gartler

1992

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

117

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The development of nearest-neighbor analysis led to the finding that the frequency of the dinucleotide CpG is markedly depressed in vertebrates. One explanation of this suppression is that methylation of CpG found in vertebrates represents a mutational hot spot through deamination of methylcytidine to thymidine. We have examined the role of methylated CpG as a factor in CpG suppression by comparing CpG distributions in coding regions of 121 genes from six species, three with methylated DNA and three with nonmethylated DNA. Overall base composition shows that all species exhibit CpG suppression, with the methylated forms showing significantly greater suppression than nonmethylated forms.When the data are analyzed by CpG position, the mean values of the methylated forms exhibit greater suppression than nonmethylated forms at positions I-II and u-m, but there is considerable overlap of suppression scores for individual species. At position nI-I, CpG suppression is marked in all methylated species, and it is reversed in all nonmethylated species. Our analysis supports the hypothesis that CpG patterns at positions u-rn and rn-I in methylated forms are affected by mutation acting through deamination of methylcytidine to thymidine. We speculate that the excess of CpGs at position III-I in nonmethylated forms may be related to a requirement for minimal thermal stability of the DNA.The development of nearest-neighbor analysis (1, 2) led to the finding that certain dinucleotides were present at frequencies that deviated significantly from random expectations. Significant deviations exist for CG vs. GC, AC vs. CA, TA vs. AT, and GT vs. TG, with the pattern of deviations being essentially uniform over a wide range of life forms (3). The frequencies of complementary dinucleotides (e.g., CG-GC) usually differ by no more than 10-20%. However, for the CG vs. GC pair in vertebrates, the difference is of the order of several hundred percent, with the dinucleotide CpG being markedly suppressed. Various ideas have been proposed to explain this CpG suppression. One explanation is based on the evidence that methylated CpG (mCpG) represents a mutational hot spot through deamination of mC to T (4-6); the C in a GpC dinucleotide is rarely, if ever, methylated (7). Other explanations consider restrictions imposed by the translation apparatus (8, 9), chromosomal structural restraints (10), and the possibility that CpG is depressed as a result of a universal coding rule (11 analyzed by CpG position a more complicated and informative picture emerges. At the first two nucleotides of a codon (position I-II) and the second two nucleotides (position II-III), the mean values of the methylated forms exhibit greater suppression than the means of the nonmethylated forms, but there is considerable overlap of suppression scores for individual species. At position III-I, CpG suppression is marked in all methylated species, and it is reversed in all nonmethylated species. To more directly examine these patterns, we identified several genes whos...

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Section: Resultsmentioning

confidence: 99%

Analysis of CpG suppression in methylated and nonmethylated species.

Schorderet

Gartler

1992

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

117

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“…16 Thus, the DNAprotein interaction in the A+T-rich region of the mtDNA has been conserved over a much longer time than has the nucleotide sequence of the same region.…”

Section: Discussionmentioning

confidence: 99%

DNA-protein interactions in theDrosophila virilismitochondrial chromosome

1984

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The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila virilis was investigated by Me3psoralen photoreaction of mitochondria isolated from embryos.After photoreaction the mtDNA was purified and the pattern of DNA cross-linking was determined by electron microscopy of the DNA under totally denaturing conditions. The transcribed regions of the mtDNA molecule contained some uncross-linked regions, but such regions were infrequent and randomly distributed. In contrast, the A+T-rich region around the origin of replication of the mtDNA was usually protected from psoralen crosslinking. The data were best fit by two protected sites, each approximately 400 base pairs, compared to the four 400 base pair sites observed in the equivalent region of D. melanogaster mtDNA [Potter et al. (1980) Proc. Nat.Acad. Sci. USA 77, [4118][4119][4120][4121][4122]. Thus this region of the mtDNA appears to be involved in a DNA-protein structure that is highly conserved even though the DNA sequence has diverged rapidly relative to protein-coding sequences.

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“…The close relationship of these species is shown by chromosome banding patterns (Lemeunier and Ashburner, 1976), gel electrophoresis (Gonzales et aL, 1982;Ohnishi et aL, 1983), and DNA sequencing (Bodmer and Ashburner, 1984;Cohn et al, 1984). D. mauritiana appears from biogeographic evidence to have arisen from a population of proto-simulans colonizing Mauritius.…”

Section: Introductionmentioning

confidence: 98%