Mechanistic role of bent DNA in transcription from eukaryotic promoters

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Unusual curved DNA structures are sometimes reported to reside within genetic regions that regulate prokaryotic and eukaryotic transcription. Extensive data suggesting a role in prokaryotic transcription for the structure have accumulated over the last few years. However, little has been revealed as to the role of DNA curvature in eukaryotic transcription.Recent studies indicated that DNA curvatures can directly activate eukaryotic transcription. In order to elucidate that mechanism, using herpes simplex thymidine kinase (tk) promoter or human adenovirus type 2 (Ad2) E1A promoter, we investigated the effects of synthetic plane and space curves on the promoter activities. Double-stranded oligonucleotides having various three-dimensional architectures were designed, synthesized and ligated to each promoter. Furthermore, rotational orientation of each synthetic DNA segment relative to each promoter was altered by deleting several nucleotides from the region between them. Luciferase assay showed that a bent DNA having left-handed superhelical writhe could remarkably activate tk promoter. In the process, rotational orientation of the writhe relative to the promoter and the distance between them played a very important role. Results of in vitro and in vivo DNase I footprinting assays indicated that introduction of synthetic DNA curvatures into upstream region of the tk promoter influenced nucleosome positioning on the promoter. The left-handed superhelical writhe directed positions of nucleosomes to prevent inappropriate inhibitory histone-DNA contacts from occurring over the TATA box. It is strongly indicated that in eukaryotic gene transcription, a role of bent DNA structures is to modulate the organization of local chromatin structure.