ACTIVE MAIZE GENES ARE UNMODIFIED AND FLANKED BY DIVERSE CLASSES OF MODIFIED, HIGHLY REPETITIVE DNA

We have characterized the copy number, organization, and genomic modif ication of DNA sequences within and flanking several maize genes. We f ound that highly repetitive DNA sequences were tightly linked to most of these genes. The highly repetitive sequences were not found within the coding regions but could be found within 6 kb either 3' or 5' to t he structural genes. These highly repetitive regions were each compose d of unique combinations of different short repetitive sequences. High ly repetitive DNA blocks were not interrupted by any detected single c opy DNA. The 13 classes of highly repetitive DNA identified were found to vary little between diverse Zea isolates. The level of DNA methyla tion in and near these genes was determined by scoring the digestibili ty of 63 recognition/cleavage sites with restriction enzymes that were sensitive to 5-methylation of cytosines in the sequences 5'-CG-3' and 5'-CNG-3'. All but four of these sites were digestible in chromosomal DNA. The four undigested sites were localized to extragenic DNA withi n or near highly repetitive DNA, while the other 59 sites were in low copy number DNAs. Pulsed field gel analysis indicated that the majorit y of cytosine modified tracts range from 20 to 200 kb in size. Single copy sequences hybridized to the unmodified domains, while highly repe titive sequences hybridized to the modified regions. Middle repetitive sequences were found in both domains.