Non-coding DNA dictates cell size and impairs fitness by sequestering RNA polymerase

Abstract Genome size varies greatly between organisms, largely because of varying amounts of non-coding DNA. In multicellular organisms, non-coding DNA can make up 99% of the genome, while unicellular organisms have little non-coding information. How non-coding DNA affects cell physiology remains a key question in understanding genome evolution. Here, we developed a system to conditionally accumulate large amounts of non-coding DNA in budding yeast cells. We show that cells adjust their size to DNA content, regardless of its coding capacity. The direct coupling of cell size to DNA content occurs independently of the known cell size control and DNA damage checkpoints and explains the long-observed correlation between cell size, genome size, and ploidy. Furthermore, we find that excess non-functional DNA compromises cell fitness and renders them hypersensitive to transcription inhibitors. Providing a potential explanation for this observation, we uncover that the transcription machinery binds non-coding DNA and is titrated away from coding genes, resulting in a reduced overall concentration of yeast transcripts. We propose that the inability of yeast to repress non-coding DNA increases the fitness cost associated with non-functional DNA and prevents its expansion in the yeast genome on evolutionary timescales.