Differential methylation of genes and repeats in land plants

Rabinowicz, P. D., Citek, R., Budiman, M. A., Nunberg, A., Bedell, J. A., Lakey, N., O'Shaughnessy, A. L., Nascimento, L. U., McCombie, W. R., Martienssen, R. A. (October 2005) Differential methylation of genes and repeats in land plants. Genome Research, 15 (10). pp. 1431-1440. ISSN 1088-9051

[thumbnail of Paper] PDF (Paper)
Differential methylation of genes.pdf - Published Version
Restricted to Repository staff only

Download (418kB)
URL: http://www.ncbi.nlm.nih.gov/pubmed/16204196
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.

Item Type: Paper
Uncontrolled Keywords: Escherichia Coli K12 K-12 DNA Methylation Maize genome Cytosine methylation rice genome transposable elements arabidopsos thaliana zea maize EVOLUTIONARY HISTORY sequence composition
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
Depositing User: CSHL Librarian
Date: October 2005
Date Deposited: 06 Jan 2012 15:31
Last Modified: 11 Apr 2013 19:48
PMCID: PMC1240086
Related URLs:
URI: https://repository.cshl.edu/id/eprint/22684

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving