In vivo transcription from multiple spacer rRNA gene promoters during early development and evolution of the intergenic spacer in the brine shrimp Artemia.

The control of ribosomal RNA (rRNA) gene expression during development can be productively studied by examination of the relationship between promoter structure and function as well as the processing of primary transcripts. Toward this end total cell RNA was extracted from embryos at various stages and probed with cloned rRNA genes using the "dot blot" method. This exercise showed that rRNA gene expression is a stage-specific process and is thus under developmental control. S1 nuclease protection experiments localized fourteen different upstream DNA sites encoding 5'-termini of pre-rRNAs during this synthetic phase of development. There is no indication of any spacer fail-safe terminator function. The S1 approach contributed to the sequencing of several of the sites. Comparative sequence alignments reveal short conserved regions in DNAs corresponding to these sites, which are shown to fall into two structural classes. Sites 3, 4, 6 and 9 are proposed to function in transcription initiation and are found to have the consensus sequence 5'...T-A-T-A-T-Pu-Pu-Pu-G-Pu-Pu-G-T-C-A 3'. Sites 1, 2, 5 and 8 which are proposed to function in 5'-processing have the consensus sequence; 5'...Pu-G-T-Pu-T-T-G 3'. These short sequence conserved regions are hypothesized to serve as recognition signals for proteins within the rDNA transcription initiation complex and for 5'-processing enzymes, respectively. Sequencing of the intergenic spacer region from which a model for spacer evolution is derived shows that tandem ca 600 bp subrepeats explain much of the multiplicity observed within control sites.