ribosomal dna deletions modulate genome-wide gene expression “rdna–sensitive” genes and natural variation核糖体dna缺失调节全基因组基因表达u201crdna-sensitiveu201d基因和自然变异.pdfVIP

Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: ‘‘rDNA–Sensitive’’ Genes and Natural Variation 1 2 2 1 2 Silvana Paredes , Alan T. Branco , Daniel L. Hartl , Keith A. Maggert *, Bernardo Lemos * 1 Department of Biology, Texas AM University, College Station, Texas, United States of America, 2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America Abstract The ribosomal rDNA gene array is an epigenetically-regulated repeated gene locus. While rDNA copy number varies widely between and within species, the functional consequences of subtle copy number polymorphisms have been largely unknown. Deletions in the Drosophila Y-linked rDNA modifies heterochromatin-induced position effect variegation (PEV), but it has been unknown if the euchromatic component of the genome is affected by rDNA copy number. Polymorphisms of naturally occurring Y chromosomes affect both euchromatin and heterochromatin, although the elements responsible for these effects are unknown. Here we show that copy number of the Y-linked rDNA array is a source of genome-wide variation in gene expression. Induced deletions in the rDNA affect the expression of hundreds to thousands of euchromatic genes throughout the genome of males and females. Although the affected genes are not physically clustered, we observed functional enrichments for genes whose protein products are located in the mitochondria and are involved in electron transport. The affected genes significantly overlap with genes affected by natural polymorphisms on Y chromosomes, suggesting that polymorphic rDNA copy number is an important determinant of