High density of an SAR-associated motif differentiates heterochromatin from euchromatin

Heterochromatin is an important component of eukaryotic chromosomes, comprising a significant portion of the total DNA in genomes. Despite its prevalence, long-standing cytological descriptions, and predominant composition of tandemly repeated DNA, no general theory unites heterochromatic with its functions. In an attempt to identify heterochromatic sequence tags, we have analysed heterochromatic sequences from Drosophila melanogaster for the presence of motifs that are known to define regions that anchor the chromosomal DNA to the scaffold (scaffold attachment regions or SARs). The SARs of Drosophila melanogaster are characterized by the presence of a small conserved sequence (the A-box) that is clustered in overall A + T-rich regions. In comparing heterochromatic and euchromatic sequences we find that heterochromatic regions are several-fold enriched for these operationally defined SARs. This high density of SAR-associated sequences not only serves as a molecular tag for heterochromatin but also suggests a hypothesis for its special properties.