title: The pattern and evolution of looped gene bendability.
abstract: 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.
authors.affiliation: Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Dai
authors.forename: Yuanyan
authors.initials: Y
authors.lastname: Xiong
authors.forename: Xianhua
authors.initials: X
authors.lastname: Dai
mesh_terms: D002843:Chromatin / Q000235:genetics*; D019143:Evolution, Molecular; D015966:Gene Expression Regulation, Fungal; D006801:Humans; D008958:Models, Molecular; D009707:Nucleosomes / Q000235:genetics*; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D013045:Species Specificity; D013728:Terminator Regions, Genetic; D035581:Transcription Factor TFIIB / Q000235:genetics*
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D035581:Transcription Factor TFIIB; D012319:RNA Polymerase II
keywords: DNA bendability; gene looping; nucleosome positioning