Identification of a genomic compartment where early replication and cytosine hypermethylation occur at nongenic regions. To highlight the loci where gene expression appeared to be behaving discordantly from the overall relationship with DNA replication and methylation, we represented early replicating and hypermethylated loci in red and low-expressing loci in green to illustrate these loci in the merged plot as orange (outlined in A). In B we show that a substantial proportion of these loci (area marked with red asterisks) have neither RefSeq nor Gencode genes annotated, nor even the lowest quintile of EST densities annotated for the UCSC Genome Browser. These loci are not only lacking any measurable gene expression, they do not even have any evidence for any transcriptional potential, regions usually referred to as gene deserts but with DNA-replication characteristics and DNase hypersensitivity (bottom right, green asterisk) that may indicate noncoding, nonprocessed transcription.
