The generation of spatial patterns of gene expression is central to metazoan development. Increasingly detailed knowledge of gene expression patterns have been gained through profiling experiments, yet the regulatory architectures and rules that define these patterns are not well understood. To address these questions, we developed a FACS-based method to purify nuclei from specific cells and then profiled and compared transcriptional and regulatory element activities in the adult germ line and four somatic tissues. We find that the majority of individual promoter and enhancer elements have tissue-specific activity and architecture, with another large class having ubiquitous activity. Specific sequence and architectural features separate promoters into two major types. Germline specific and ubiquitously active promoters have well positioned -1/+1 nucleosomes and a 10bp TT periodicity immediately downstream of the transcription start site. Promoters only active in somatic tissues lack these features and exhibit a wider nucleosome-depleted region. We also identified specific motifs and transcription factors associated with either germline or somatic promoters. Our datasets can be obtained and explored via our tissue-specific genome browser at
http://ahringerlab.com. Our results show that there are fundamental differences between germ line and somatic promoters and uncover regulatory rules for generating diverse gene expression patterns.