A cell-free RNA polymerase I transcription system was used to evaluate the transcription efficiency of 21 linker scanning mutations that span the human rRNA gene promoter. Our analysis revealed the presence of two major control elements, designated the core and upstream elements, that affect the level of transcription initiation. The core element extends from -45 to +18 relative to the RNA start site, and transcription is severely affected (up to 100-fold) by linker scanning mutations in this region. Linker scanning and deletion mutations in the upstream element, located between nucleotides -156 and -107, cause a three-to fivefold reduction in transcription. Under certain reaction conditions, such as the presence of a high ratio of protein to template or supplementation of the reaction with partially purified protein fractions, sequences upstream of the core element can have an even greater effect (20-to 50-fold) on RNA polymerase I transcription. Primer extension analysis showed that RNA synthesized from all of these mutant templates is initiated at the correct in vivo start site. To examine the functional relationship between the core and the upstream region, mutant promoters were constructed that alter the orientation, distance, or multiplicity of these control elements relative to each other. The upstream control element appears to function in only one orientation, and its position relative to the core is constrained within a fairly narrow region. Moreover, multiple core elements in close proximity to each other have an inhibitory effect on transcription.The cellular machinery responsible for RNA synthesis is designed to respond to a variety of specific signals so that genes can be transcribed and expressed in a controlled fashion. For example, the synthesis of rRNA is sensitive to a variety of physiological signals such as response to nutrient starvation, regulation by cell cycle, the state of cell proliferation, and invasion by viral infection (6,9,17,24,26,27,31). In addition, an interesting and unexpected property of rRNA transcription is the inability of the transcriptional machinery of one species to initiate transcription from the promoter of divergent species. Thus, whereas both sets of rRNA genes can be transcribed in an interspecific rodent cell hybrid, the genes from only one species are expressed in rodent-human cell hybrids (22,32). This species specificity is mimicked in vitro in that extracts from one species are capable of transcribing only those rDNA templates that are derived from the same or closely related species (5,12,14). The limited homology in the DNA sequence surrounding the transcription start site of mammalian rRNA genes suggests that species-specific promoter recognition is likely to involve distinctive rRNA promoter elements.Studies with fractionated enzyme components derived from mammalian cell extracts have allowed the identification of at least two distinct activities that are necesary to reconstitute accurate and efficient initiation of transcription from the human ribosomal...