Differential methylation of genes and repeats in land plants

• Published in: Genome research Vol. 15; no. 10; pp. 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: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.10.2005
• Subjects: DNA Methylation; Gene Duplication; Genes, Plant; Letters; Molecular Sequence Data; Phylogeny; Polyploidy; Repetitive Sequences, Nucleic Acid; Sorghum; Triticum aestivum; Zea mays
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.4100405

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.