Inverted repeats (IR) play important roles in specific DNA-dependent processes in simple prokaryotes to complex eukaryotes. They are recognized by a variety of proteins including restriction enzymes, helicases and transcription factors. We evaluate the presence and localization of IRs in all validated human promoter sequences within 1000 bp upstream and downstream of the transcription start site (TSS). The occurrence of 7 bp and longer IRs is located non-randomly in promoter regions, with enrichment within 200 bp upstream of the TSS. The highest frequency of IRs is just before TSS for repeats of 8 bp or longer. A comparison of promoters divided according to the occurrence of five individual promoter motifs shows unique location patterns of IRs. Principal component analyses and hierarchical clustering of IRs abundance demonstrated that they are depleted and/or not enriched in the promoters of stably expressed genes, but show significant enrichments for specific dynamically regulated biological pathways.

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 Brno 612 65 Czech Republic

Mendel University in Brno Zemědělská 1 Brno 613 00 Czech Republic

Citace poskytuje Crossref.org

Non-canonical DNA structures in the human ribosomal DNA

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids