Analysis of the amplification promoting sequence (EXP) in the ribosomal RNA gene

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The ribosomal RNA gene repeats (rDNA) is one of the most characteristic regions in eukaryotic chromosomes. The repeats consist of more than 100 tandem units occupying large part of the chromosome in most of organisms. Repeated genes families such as the ribosomal RNA genes (rDNA) are thought to be fragile sites for deletional recombination. However, as for the rDNA, cells have gene amplification system and recover copy number to the wild type level. We found a cis-essential sequence (EXP) for the amplification. In this research, I analyzed molecular mechanism of the EXP.First, we did the phylogenetic footprinting assay in the EXP using several kinds of yeasts and found a conserved region. Interestingly, the region was a bi-directional noncoding transcriptional promoter that is reported〜20 years ago. We tested the character of the promoter and found the transcription was essential for the amplification. Interestingly, when the rDNA copy number reduces, the transcription is activated and it removes cohesin from the region. As the result, unequal sister-chromatid recombination increases and amplification is induced. Then, when the copy number reaches around the wild type level, Sir2 protein represses the transcription and by the function of recovered cohesin the unequal sister-chromatid recombination is restricted. Like these, we found the copy number regulation system, that is, Sir2 regulates rDNA copy number through E-pro transcription by changing cohesin association.