Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin

We have used line HS-2 of Drosophila melanogaster, carrying a silenced tran sgene in the pericentric heterochromatin, to investigate in detail the chro matin structure imposed by this environment. Digestion of the chromatin wit h micrococcal nuclease (MNase) shows a nucleosome array with extensive long -range order, indicating regular spacing, and with well-defined MNase cleav age fragments, indicating a smaller MNase target in the linker region. The repeating unit is ca. 10 bp larger than that observed for bulk Drosophila c hromatin, The silenced transgene shows both a loss of DNase I-hypersensitiv e sites and decreased sensitivity to DNase I digestion within an array of n ucleosomes lacking such sites; within such an array, sensitivity to digesti on by MNase is unchanged. The ordered nucleosome array extends across the r egulatory region of the transgene, a shift that could explain the loss of t ransgene expression in heterochromatin, Highly regular nucleosome arrays ar e observed over several endogenous heterochromatic sequences, indicating th at this is a general feature of heterochromatin, However, genes normally ac tive within heterochromatin (rolled and light) do not show this pattern, su ggesting that the altered chromatin structure observed is associated with r egions that are silent, rather than being a property of the domain as a who le. The results indicate that long-range nucleosomal ordering is linked wit h the heterochromatic packaging that imposes gene silencing.