5-Methylcytosine content and methylation status in six millet DNAs

Kumar, Lalitha Sunil; Hendre, R.R.; Ranjekar, P. K.

doi:10.1007/bf02704712

Cited by 2 publications

(2 citation statements)

References 19 publications

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“…Interpretation of the condition IV (absence from both MseI-HpaII and MseI-MspI products) as informative, missing or null data modified the relationship between HPLC estimates and the quantitative interpretations of MSAP results. Kumar et al (1990) Estimates obtained by chromatographic quantification (HPLC) of individual nucleosides are typically expressed as percentage of global cytosines that are methylated [%mC = 100 * mC/(C + mC)]. Analyses of fragment size polymorphisms obtained by endonucleases differing in mC sensitivity (MSAP) were more variable in their way of reporting results.…”

Section: Helleborus Foetidus: Msap Analyses and Comparisons With Hplcmentioning

confidence: 99%

“…Regarding the adequacy of combining condition II and III markers, it is important to emphasize that the relative contribution of CG, CHG and CHH contexts to global cytosine content estimates varies across plant species (Gruenbaum et al 1981;Belanger & Hepburn 1990;Kumar et al 1990;Kova r ık et al 1997). In addition, we found that percentages of methylation at CG and CHG contexts varied among species (Table 1; see also Feng et al 2010;Zhong et al 2013), thus suggesting that analyses of methylation at different contexts may be useful to reveal species-specific aspects.…”

Section: Msap Analyses and Global Cytosine Methylation Estimates In Hmentioning

confidence: 99%

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MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild‐growing species

Alonso

Pérez

Bazaga

et al. 2015

Molecular Ecology Resources

108

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Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cytosine methylation in genomic DNA obtained by HPLC analysis. A screening of literature revealed that methylation of cytosines at cleavage sites assayed by MSAP was greater than genome-wide estimates obtained by HPLC, and percentages of methylation at different nucleotide contexts varied within and across species. Concurrent HPLC and MSAP analyses of DNA from 200 individuals of the perennial herb Helleborus foetidus confirmed that methyl-cytosine was more frequent in CCGG contexts than in the genome as a whole. In this species, global methylation was unrelated to methylation at the inner CG site. We suggest that global HPLC and context-specific MSAP methylation estimates provide complementary information whose combination can improve our current understanding of methylation-based epigenetic processes in nonmodel plants.

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Section: Helleborus Foetidus: Msap Analyses and Comparisons With Hplcmentioning

confidence: 99%

Section: Msap Analyses and Global Cytosine Methylation Estimates In Hmentioning

confidence: 99%

MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild‐growing species

Alonso

Pérez

Bazaga

et al. 2015

Molecular Ecology Resources

108

View full text Add to dashboard Cite

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Molecular and physical organization of highly repetitive, undermethylated DNA from Pennisetum glaucum

1994

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A HaeIII monomer of a repetitive DNA family from Pennisetum glaucum (L.) R. Br. cv. Massue has been cloned and characterized. The repeat is 137 bp long and is organized in head-to-tail orientation in tandem arrays. The HaeIII monomer contains 55% A+T residues. The distribution of this highly repetitive sequence in different Pennisetum species and in other cereals was investigated. The HaeIII satellite is present in all Pennisetum species investigated but absent from other genera examined. In situ hybridization revealed a centromeric localization of this sequence on all seven chromosome pairs and indicated chromosome-specific differences in copy number. Methylation was investigated by comparative restriction enzyme analysis (MspI/HpaII) which showed a greater extent of methylation of the internal C of the enzyme recognition site 5'-CCGG. A South-Western analysis, using an anti-methylcytosine antibody to examine the methylation status in P. glaucum confirmed that the sequence is not highly methylated.

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5-Methylcytosine content and methylation status in six millet DNAs

Cited by 2 publications

References 19 publications

MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild‐growing species

MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild‐growing species

Molecular and physical organization of highly repetitive, undermethylated DNA from Pennisetum glaucum

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