e-journal

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

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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.

Keywords: DNA methylation, epigenetics, Helleborus foetidus, high-performance liquid chromatography, methyl-cytidine, methylation-sensitive amplification polymorphism, plant adaptation, population ecology, Ranunculaceae, stress

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Ketersediaan

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Informasi Detail

Judul Seri

Molecular Ecology Resources

No. Panggil

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Penerbit

New York : John Wiley & Sons, Ltd.., 2016

Deskripsi Fisik

Molecular Ecology Resources (2016) 16, 80–90

Bahasa

English

ISBN/ISSN

doi: 10.1111/1755-09

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

(2016) 16

Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

agus

Versi lain/terkait

Lampiran Berkas

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