Synthetic expansion of non-coding DNA reveals physiological constraints on genome size

Genome size varies widely across eukaryotes, largely because of differences in non-coding DNA, but the physiological consequences of this variation remain unclear. To directly test how non-coding DNA abundance influences cellular physiology, we engineered a scalable genome-expansion system in the budding yeast S. cerevisiae that increases genome size while leaving the endogenous genome unchanged. By sequentially fusing yeast artificial chromosomes (YACs) carrying predominantly non-coding human DNA, we generated strains with up to 12.8 Mb of additional DNA, approximately doubling the native genome. Genome expansion reduced growth rate and increased cell size in proportion to the amount of non-coding DNA. Spike-in-normalized RNA-seq and ChIP-seq revealed that the non-coding DNA is pervasively transcribed, with a proportional amount of RNA polymerase II being redistributed from the endogenous genome to the added non-coding sequences. This resulted in a global decrease in the endogenous mRNA concentration. However, ribosome profiling and proteomics experiments revealed that there is little translation of YAC-associated transcripts. Our mathematical model shows that cellular growth rate decreases because non-coding DNA acts as a sink for transcriptional resources to lower the concentration of endogenous mRNA. Thus, our work links genome expansion to proliferative capacity and offers a mechanistic explanation for why the fastest-growing cells, such as yeast and bacteria, carry so little non-coding DNA.