Gene looping, defined as the physical interaction between the promoter and 
terminator regions of a RNA polymerase II-transcribed gene, is widespread in 
yeast and mammalian cells. Gene looping has been shown to play important roles 
in transcription. Gene-loop formation is dependent on regulatory proteins 
localized at the 5' and 3' ends of genes, such as TFIIB. However, whether other 
factors contribute to gene looping remains to be elucidated. Here, we 
investigated the contribution of intrinsic DNA and chromatin structures to gene 
looping. We found that Saccharomyces cerevisiae looped genes show high DNA 
bendability around middle and 3/4 regions in open reading frames (ORFs). This 
bendability pattern is conserved between yeast species, whereas the position of 
bendability peak varies substantially among species. Looped genes in human cells 
also show high DNA bendability. Nucleosome positioning around looped ORF middle 
regions is unstable. We also present evidence indicating that this unstable 
nucleosome positioning is involved in gene looping. These results suggest a 
mechanism by which DNA bendability and unstable nucleosome positioning could 
assist in the formation of gene loops.