Synthetic reversed sequences reveal default genomic states

Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or ‘noise’1,2,3,4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in ‘default genomic states’ between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes. Synthetic loci were characterized in yeast using ATAC-seq, RNA-seq, CAGE-seq, and CUT&RUN for H3K4me3, and in mESCs using ATAC-seq, RNA-seq, and CUT&RUN for H3K4me3, H3K27ac, H3K27me3, and RNAP2. HPRT1 and HPRT1R were characterized in yeast as episomes and following genomic integration. In mESCs, HPRT1 was characterized in mESCs at one integration site on chrX, and HPRT1R and HPRT1RnoCpG were characterized at two integration sites each, on chrX and chr3. Two independent clones were characterized for each synthetic locus integration, and two replicates were performed for each clone.