Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography

Wagner, Isaac D.; Capesius, Ingrid

doi:10.1016/0005-2787(81)90135-0

Cited by 116 publications

(71 citation statements)

References 17 publications

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“…Indeed, methylation of DNA molecules decreases their buoyant densities by 0.7 g͞cm 3 per 1% of 5-methylcytosine (17)(18)(19), and fractions corresponding to the gene spaces of some of the Gramineae studied here are characterized by different levels of 5-methylcytosine (20,21).…”

Section: Discussionmentioning

confidence: 93%

The distribution of genes in the genomes of Gramineae

Barakat

Carels

Bernardi

1997

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

143

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Recent investigations showed that most maize genes are present in compositional fractions of nuclear DNA that cover only a 1-2% GC (molar fraction of guanosine plus cytosine in DNA) range and represent only 10-20% of the genome. These fractions, which correspond to compositional genome compartments that are distributed on all chromosomes, were collectively called the ''gene space.'' Outside the gene space, the maize genome appears to contain no genes, except for some zein genes and for ribosomal genes. Here, we investigated the distribution of genes in the genomes of two other Gramineae, rice and barley, and used a new set of probes to study further the gene distribution of maize. We found that the distribution of genes in these three genomes is basically similar in that all genes, except for ribosomal genes and some storage protein genes, were located in gene spaces that (i) cover GC ranges of 0.8%, 1.0%, and 1.6% and represent 12%, 17%, and 24% of the genomes of barley, maize, and rice, respectively; (ii) are due to a remarkably uniform base composition in the sequences surrounding the genes, which are now known to consist mainly of transposons; (iii) have sizes approximately proportional to genome sizes, suggesting that expansion-contraction phenomena proceed in parallel in the gene space and in the gene-empty regions of the genome; and (iv) only hybridize on the gene spaces (and not on the other DNA fractions) of other Gramineae.Previous investigations on angiosperms showed that their nuclear genomes are characterized by a compositional compartmentalization (1, 2) and that their nuclear genes may be contained in compositional compartments that cover only a narrow GC (molar fraction of guanosine plus cytosine in DNA) range (3). Recent work on the distribution of genes in the nuclear genome of maize (4) showed that the 20 probes used localized genes in compositional compartments (collectively called the gene space) that covered a 1-2% GC range and represented 10-20% of total nuclear DNA. Some zein genes detected by the zein probe used and ribosomal genes were, however, located in compartments lower and higher in GC, respectively, compared with all other protein-encoding genes tested. The gene distribution of the maize genome is very different from that found in the human genome. Indeed, the latter, which has a comparable haploid size and a similar compositional distribution of DNA molecules and coding sequences, has its genes distributed over its entire 30% GC range, although in a remarkably nonuniform way, most genes being located in the GC-rich regions of the genomes (5-7).A question raised by the existence of the gene space of the maize genome is whether this particular gene distribution is shared by other plants of the family Gramineae (or Poaceae) and by other angiosperms. Here, we report results obtained for rice (from the Oryza group of the subfamily Bambooideae) and for barley (from the Triticum group of the subfamily Pooideae) and show that they are similar to those found in maize (from the Ze...

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Section: Discussionmentioning

confidence: 93%

The distribution of genes in the genomes of Gramineae

Barakat

Carels

Bernardi

1997

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

143

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“…(Leutwiler eta/., 1984); tobacco (Messeguer, et a/., 1991); pea, wheat (Wagner and Capesius, 1981); maize (Ergle and Katternrnan, 1961). Clip is the expected average fragment length where p is the probability of cleavage per nucleotide (Seed, eta/., 1982).…”

Section: Methylation Sensitivity Of Hpall Mspl and Acclllmentioning

confidence: 99%

^mCCG methylation in angiosperms

Jeddeloh

Richards²

1996

The Plant Journal

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“…the level of DNA methylation, have been found among different plant species (9,14,17,19,20 (Fig. 1).…”

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confidence: 93%

Specific Levels of DNA Methylation in Various Tissues, Cell Lines, and Cell Types of Daucus carota

Palmgren

Mattsson²,

Okkels³

1991

Plant Physiol.

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The level of DNA methylation in Daucus carota was found to be tissue specific, but no simple correlation between developmental stage or age of tissue and the level of DNA methylation was found. Among three different suspension culture lines from the same variety grown under identical conditions, large differences in the level of DNA methylation were observed. The highest and lowest levels were found in two embryogenic cell lines originating from the same clone. Suspension cells from one of the embryogenic cell lines were fractionated into three morphologically defined cell types using Percoll gradient density centrifugation, and the uniformity of these fractions was evaluated by image analysis. The three cell types showed different levels of DNA methylation. The lowest level was found in the fraction containing the precursor cells of somatic embryos.(Uppsala, Sweden). The suspension culture cell lines N04, NR, and NR2 were established from seedlings of the "Nobo" variety (Danefeldt, Odense, Denmark). They were initiated and kept as previously described (14). Somatic embryos were obtained by washing cells three times in Gamborg B5 medium (7) without hormones and diluting the cells to 10% settled cell volume. They were then plated on the same medium with 0.7% (w/v) agarose (type I, Sigma) and kept in the light for 7 d or until globular somatic embryos had emerged.Isolation of DNA and Determination of the Level of DNA Methylation DNA was isolated and further purified and the level of DNA methylation was determined as previously described (14). Briefly, DNA was digested by nuclease P1 and bacterial alkaline phosphatase and the resulting deoxyribonucleosides were separated and quantified by HPLC. mdC2 is present in DNA ofall higher organisms investigated (5, 15). DNA methylation is involved in regulation of gene activity and differentiation, and normally methylation of a gene inactivates its transcription (4, 6). In plants, it has been shown that in tissues, where a gene is expressed, it is often hypomethylated in comparison to tissues, where it is not expressed (1, 2, 16).

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Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography

Cited by 116 publications

References 17 publications

The distribution of genes in the genomes of Gramineae

The distribution of genes in the genomes of Gramineae

^mCCG methylation in angiosperms

Specific Levels of DNA Methylation in Various Tissues, Cell Lines, and Cell Types of Daucus carota

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