The importance of DNA structure in the regulation of basic cellular processes is an emerging field of research. Among local non-B DNA structures, inverted repeat (IR) sequences that form cruciforms and G-rich sequences that form G-quadruplexes (G4) are found in all prokaryotic and eukaryotic organisms and are targets for regulatory proteins. We analyzed IRs and G4 sequences in the genome of the most important biotechnology microorganism, S. cerevisiae. IR and G4-prone sequences are enriched in specific genomic locations and differ markedly between mitochondrial and nuclear DNA. While G4s are overrepresented in telomeres and regions surrounding tRNAs, IRs are most enriched in centromeres, rDNA, replication origins and surrounding tRNAs. Mitochondrial DNA is enriched in both IR and G4-prone sequences relative to the nuclear genome. This extensive analysis of local DNA structures adds to the emerging picture of their importance in genome maintenance, DNA replication and transcription of subsets of genes.

Brno University of Technology Faculty of Chemistry Purkyňova 118 612 00 Brno Czech Republic

Brno University of Technology Faculty of Chemistry Purkyňova 118 612 00 Brno Czech Republic; Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 612 65 Brno Czech Republic

Brno University of Technology Faculty of Mechanical Engineering Technická 2896 2 616 69 Brno Czech Republic

Brno University of Technology Faculty of Mechanical Engineering Technická 2896 2 616 69 Brno Czech Republic; Mendel University in Brno Zemědělská 1665 1 61300 Brno Czech Republic

Department of Biology and Ecology Institute of Environmental Technologies Faculty of Science University of Ostrava Ostrava 710 00 Czech Republic

Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 612 65 Brno Czech Republic

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