Genome organization and characterization of the repetitive and inverted repeat DNA sequences in Neurospora crassa.

Regulatory circuits have been defined in Neurospora c m s a within which multiple unlinked genes are controlled in a positive fashion by major regulatory genes. It has been suggested that repetitive DNA sequences situated adjacent to structural genes may serve as regulatory sites. Experiments are presented which examine the amount and organization of the repetitive sequences of Neurospora. The genome consists of 2.7 X 10’ base pairs and is composed of 2% foldback, 8% repetitive, and 90% single copy sequences. Our results indicate that the repeated DNA sequences are organized in stretches of 10,000 base pairs or longer. Experiments using pure ribosomal DNA isolated from cloned recombinant DNA demonstrated that rDNA represents 7% of total nuclear DNA and 88% of the repetitive component. The rDNA sequence is repeated about 185 times per nucleus. Since the ribosomal DNA units are believed to be tandemly repeated many times, their clustering can largely account for the long repetitive stretches and their lack of interspersion with single copy DNA. These results argue that repetitive DNA sequences identified by renaturation experiments do not serve a regulatory function in Neurospora. About 350 foci of inverted repeat, or foldback, DNA sequences occur in the genome and are interspersed with single copy DNA. The relatively small number of foldback foci suggest that inverted repeats also cannot be the primary recognition elements for control of gene expression in Neurospora. We suggest that very short repeated sequences, undetected by renaturation experiments, may serve as recognition sites for eukaryotic gene regulation.