Differential methylation of genes and repeats in land plants

The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration (MF). Therefore, MF has been used as a gene enrichment technology in sorghum and maize, where gene enrichment was proportional to genome size. Here we apply MF to a br...

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Bibliographic Details
Published in:Genome research 2005-10, Vol.15 (10), p.1431-1440
Main Authors: Rabinowicz, Pablo D, Citek, Robert, Budiman, Muhammad A, Nunberg, Andrew, Bedell, Joseph A, Lakey, Nathan, O'Shaughnessy, Andrew L, Nascimento, Lidia U, McCombie, W Richard, Martienssen, Robert A
Format: Article
Language:English
Subjects:
DNA Methylation
Gene Duplication
Genes, Plant
Letters
Molecular Sequence Data
Phylogeny
Polyploidy
Repetitive Sequences, Nucleic Acid
Sorghum
Triticum aestivum
Zea mays
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Summary:The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration (MF). Therefore, MF has been used as a gene enrichment technology in sorghum and maize, where gene enrichment was proportional to genome size. Here we apply MF to a broad variety of plant species spanning a wide range of genome sizes. Differential methylation of genic and non-genic sequences was observed in all species tested, from non-vascular to vascular plants, but in some cases, such as wheat and pine, a lower than expected level of enrichment was observed. Remarkably, hexaploid wheat and pine show a dramatically large number of gene-like sequences relative to other plants. In hexaploid wheat, this apparent excess of genes may reflect an abundance of methylated pseudogenes, which may thus be more prevalent in recent polyploids.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.4100405