Isolation of Plant Gene Space-Related Sequence Elements by High C+G Patch (HCGP) Filtration: Model Study on Rice

• Published in: Plant molecular biology reporter Vol. 27; no. 1; pp. 79 - 85
• Main Authors: Berenyi, M, Mauleon, R. P, Kopecky, D, Wandl, S, Friedl, R, Fluch, S, Boonruangrod, R, Muge, E, Burg, K
• Format: Journal Article
• Language: English
• Published: New York New York : Springer-Verlag 2009; Springer-Verlag; Springer Nature B.V
• Subjects: Bioinformatics; Biomedical and Life Sciences; Cloning; Deoxyribonucleic acid; DNA; DNA fragmentation; DNA methylation; Filtration; Fragmentation; Gene sequencing; genetic techniques and protocols; Genomes; Life Sciences; Metabolomics; molecular cloning; new methods; Oryza; Oryza sativa; Plant Breeding/Biotechnology; Plant Sciences; Proteomics; restriction endonucleases; Gene filtration; High C+G content; Gene space; HCGP filtration; CCGG cutters
• ISSN: 0735-9640; 1572-9818
• DOI: 10.1007/s11105-008-0063-2

For the isolation of gene space representative sequence elements, a new methodology--high C+G patch (HCGP) filtration--has been developed using rice as a model. The method is based on the fragmentation of the genomic DNA by methylation-sensitive HpaII and MspI restriction endonucleases having exclusively G/C base pair-containing recognition sites. These enzymes fragment the genome at high C+G content and hypomethylated regions. Cloning fragments spanning such regions in close vicinity (200-2,000 bp) revealed that about 60% of the clones represented gene space sequences resulting in twofold enrichment of these sequences, which is close to the theoretical maximum in rice.