Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome

Rabinowicz, P. D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L. D., Stein, L., McCombie, W. R., Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics, 23 (3). pp. 305-308. ISSN 10614036 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/10545948
DOI: 10.1038/15479

Abstract

The genomes of higher plants and animals are highly differentiated, and are composed of a relatively small number of genes and a large fraction of repetitive DNA. The bulk of this repetitive DNA constitutes transposable, and especially retrotransposable, elements. It has been hypothesized that most of these elements are heavily methylated relative to genes, but the evidence for this is controversial. We show here that repeat sequences in maize are largely excluded from genomic shotgun libraries by the selection of an appropriate host strain because of their sensitivity to bacterial restriction-modification systems. In contrast, unmethylated genic regions are preserved in these genetically filtered libraries if the insert size is less than the average size of genes. The representation of unique maize sequences not found in plant reference genomes is also greatly enriched. This demonstrates that repeats, and not genes, are the primary targets of methylation in maize. The use of restrictive libraries in genome shotgun sequencing in plant genomes should allow significant representation of genes, reducing the number of reactions required.

Item Type: Paper
Uncontrolled Keywords: DNA article gene insertion gene library gene sequence genome maize methylation nonhuman priority journal retroposon sequence analysis Cloning, Molecular DNA Methylation DNA Restriction Enzymes Escherichia coli Genes, Plant Genome, Plant Genomic Library Molecular Sequence Data Nucleic Acid Hybridization Retroelements Sequence Analysis, DNA Sequence Homology, Nucleic Acid Zea mays Animalia Bacteria (microorganisms) Embryophyta
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
CSHL labs > Stein lab
Depositing User: Matt Covey
Date Deposited: 25 Apr 2013 19:51
Last Modified: 25 Apr 2013 19:51
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28208

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