Synthetic reversed sequences reveal default genomic states

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Pervasive transcriptional activity is a common feature across species, but its origin (selection vs. noise) remains debated.
• Understanding default genome states is crucial to determine the biological significance of widespread transcription.

Purpose of the Study:

• To investigate whether synthetic genomic sequences, devoid of evolved coding or regulatory information, exhibit transcriptional activity.
• To compare the 'default genomic state' in Saccharomyces cerevisiae (yeast) and Mus musculus (mouse) embryonic stem cells.

Main Methods:

• Introduction of a synthetic 101-kb locus, based on reversed human HPRT1, into yeast and mouse genomes.
• Characterization of genomic activity and chromatin signatures of the synthetic locus in both species.
• Analysis of a variant locus lacking CpG dinucleotides to assess its impact on activity.

Main Results:

• Widespread transcriptional activity of the synthetic locus was observed in yeast, even without native promoters.
• The synthetic locus was transcriptionally inactive in mouse embryonic stem cells, displaying repressive chromatin signatures.
• A CpG-depleted variant also remained transcriptionally inactive in mouse cells, despite alleviated repressive signatures.

Conclusions:

• Synthetic, non-coding DNA sequences exhibit distinct transcriptional behaviors in yeast versus mouse cells, indicating divergent default genomic states.
• These findings suggest that pervasive transcription may not be solely 'noise' and have implications for horizontal gene transfer and the emergence of new genes.