Transgenes are important tools for plant molecular biologists. However, some aspects of their regulation are not completely understood. First, the contribution of elements separate from the promoter has been documented for several genes, but a general requirement for such elements is still unclear. Second, transgene expression can be subject to variability from chromosomal position effects and from epigenetic effects, often due to the presence of repeated sequences. While studying the regulation of the developmentally expressed Heat Shock Cognate 80 (HSC80) gene, several peculiarities were found which involve both of these questions. First, HSC80 transgenes are subject to silencing and variegation at a high frequency. Second, a bipartite element downstream of the transcriptional start is necessary to achieve efficient expression from the HSC80 promoter in stable transformants. Finally, this bipartite element is not required for expression in a transient system, where the promoter alone is sufficient. These results together support a role for chromatin structure in the regulation of HSC80.